Starting phenix.real_space_refine on Tue Nov 14 07:27:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/11_2023/7zt6_14955_updated.pdb" } resolution = 3.5 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= 0.008 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5175 2.51 5 N 1363 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 428": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 8073 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3863 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 27, 'TRANS': 473} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4174 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.61 Number of scatterers: 8073 At special positions: 0 Unit cell: (88.02, 92.584, 132.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1491 8.00 N 1363 7.00 C 5175 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: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 7 sheets defined 32.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.075A pdb=" N PHE A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 511 through 529 removed outlier: 6.496A pdb=" N SER A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 200 through 222 removed outlier: 7.834A pdb=" N GLU B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASP B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.982A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 520 through 536 removed outlier: 4.819A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 199 through 204 removed outlier: 3.617A pdb=" N ARG A 165 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 82 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE A 40 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA A 84 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 42 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 86 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.536A pdb=" N TYR A 369 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 409 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 349 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 318 through 322 Processing sheet with id= D, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.982A pdb=" N GLU B 53 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 10 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 129 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL B 11 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 131 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS B 13 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU B 133 " --> pdb=" O CYS B 13 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP B 15 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 135 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 160 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE B 134 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN B 162 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 249 through 253 removed outlier: 3.587A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 344 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 313 through 316 Processing sheet with id= G, first strand: chain 'B' and resid 464 through 467 removed outlier: 4.481A pdb=" N THR B 472 " --> pdb=" O ASP B 467 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 846 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: 2.20 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2576 1.34 - 1.46: 1274 1.46 - 1.57: 4319 1.57 - 1.69: 6 1.69 - 1.81: 64 Bond restraints: 8239 Sorted by residual: bond pdb=" O12 IHP A 701 " pdb=" P2 IHP A 701 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O15 IHP A 701 " pdb=" P5 IHP A 701 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O16 IHP A 701 " pdb=" P6 IHP A 701 " ideal model delta sigma weight residual 1.672 1.603 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C MET A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N ARG A 444 " pdb=" CA ARG A 444 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.56e+00 ... (remaining 8234 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.46: 196 105.46 - 112.62: 4464 112.62 - 119.78: 2509 119.78 - 126.95: 3897 126.95 - 134.11: 83 Bond angle restraints: 11149 Sorted by residual: angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 113.41 108.08 5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.88 107.28 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" C LYS B 481 " ideal model delta sigma weight residual 113.23 108.09 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" O ILE B 482 " ideal model delta sigma weight residual 119.71 115.91 3.80 9.30e-01 1.16e+00 1.67e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" N PRO B 483 " ideal model delta sigma weight residual 119.15 123.56 -4.41 1.20e+00 6.94e-01 1.35e+01 ... (remaining 11144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4607 17.56 - 35.12: 350 35.12 - 52.69: 61 52.69 - 70.25: 16 70.25 - 87.81: 6 Dihedral angle restraints: 5040 sinusoidal: 2015 harmonic: 3025 Sorted by residual: dihedral pdb=" CA GLU B 199 " pdb=" C GLU B 199 " pdb=" N GLN B 200 " pdb=" CA GLN B 200 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET B 14 " pdb=" C MET B 14 " pdb=" N ASP B 15 " pdb=" CA ASP B 15 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS A 510 " pdb=" C LYS A 510 " pdb=" N VAL A 511 " pdb=" CA VAL A 511 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1126 0.074 - 0.148: 134 0.148 - 0.222: 5 0.222 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 1267 Sorted by residual: chirality pdb=" C1 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O11 IHP A 701 " both_signs ideal model delta sigma weight residual False 2.32 2.69 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C5 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O15 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.42 -2.66 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" O13 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.55 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1264 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 71 " 0.014 2.00e-02 2.50e+03 1.12e-02 2.52e+00 pdb=" CG TYR A 71 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 71 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 71 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 161 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C MET A 161 " -0.022 2.00e-02 2.50e+03 pdb=" O MET A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 162 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 199 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU B 199 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU B 199 " -0.007 2.00e-02 2.50e+03 pdb=" N GLN B 200 " -0.007 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 986 2.74 - 3.28: 8771 3.28 - 3.82: 13780 3.82 - 4.36: 15816 4.36 - 4.90: 26387 Nonbonded interactions: 65740 Sorted by model distance: nonbonded pdb=" OD1 ASP B 467 " pdb=" OG1 THR B 472 " model vdw 2.203 2.440 nonbonded pdb=" O ASP B 116 " pdb=" ND1 HIS B 120 " model vdw 2.221 2.520 nonbonded pdb=" OG SER B 348 " pdb=" OD2 ASP B 388 " model vdw 2.229 2.440 nonbonded pdb=" OE2 GLU A 371 " pdb=" OG SER A 373 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 361 " pdb=" O GLY B 358 " model vdw 2.236 2.440 ... (remaining 65735 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 5.810 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 : 0.006 0.080 8239 Z= 0.393 Angle : 0.707 8.637 11149 Z= 0.389 Chirality : 0.045 0.369 1267 Planarity : 0.003 0.027 1424 Dihedral : 13.247 87.810 3070 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1025 helix: 1.84 (0.29), residues: 328 sheet: -0.65 (0.39), residues: 167 loop : -0.55 (0.28), residues: 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 1.032 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 0.1899 time to fit residues: 13.2217 Evaluate side-chains 33 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0688 time to fit residues: 1.4940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 0.0980 chunk 41 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8239 Z= 0.135 Angle : 0.541 7.890 11149 Z= 0.268 Chirality : 0.041 0.146 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.547 26.539 1105 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.47 % Allowed : 5.58 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1025 helix: 1.87 (0.29), residues: 337 sheet: -0.40 (0.40), residues: 162 loop : -0.51 (0.28), residues: 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 1.003 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.1602 time to fit residues: 10.1062 Evaluate side-chains 33 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0988 time to fit residues: 1.5341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8239 Z= 0.118 Angle : 0.494 6.782 11149 Z= 0.247 Chirality : 0.040 0.140 1267 Planarity : 0.003 0.021 1424 Dihedral : 4.237 24.752 1105 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.12 % Allowed : 9.53 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1025 helix: 1.96 (0.29), residues: 330 sheet: -0.34 (0.41), residues: 162 loop : -0.49 (0.28), residues: 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.003 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1632 time to fit residues: 10.0622 Evaluate side-chains 31 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8239 Z= 0.350 Angle : 0.583 6.936 11149 Z= 0.291 Chirality : 0.039 0.134 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.294 22.329 1105 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.47 % Allowed : 11.63 % Favored : 87.91 % 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: 0.62 (0.27), residues: 1025 helix: 2.07 (0.29), residues: 336 sheet: -0.41 (0.39), residues: 169 loop : -0.37 (0.29), residues: 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 1.053 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1632 time to fit residues: 9.5236 Evaluate side-chains 34 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0810 time to fit residues: 1.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 0.0670 chunk 41 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8239 Z= 0.232 Angle : 0.519 6.727 11149 Z= 0.260 Chirality : 0.039 0.136 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.216 21.343 1105 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.47 % Allowed : 11.63 % Favored : 87.91 % 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: 0.62 (0.27), residues: 1025 helix: 2.05 (0.29), residues: 337 sheet: -0.40 (0.41), residues: 162 loop : -0.37 (0.29), residues: 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 1.563 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1690 time to fit residues: 10.3068 Evaluate side-chains 34 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0819 time to fit residues: 1.6588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.0010 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8239 Z= 0.134 Angle : 0.511 7.869 11149 Z= 0.250 Chirality : 0.039 0.139 1267 Planarity : 0.002 0.025 1424 Dihedral : 4.072 20.205 1105 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.35 % Allowed : 12.67 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1025 helix: 2.18 (0.29), residues: 330 sheet: -0.35 (0.41), residues: 162 loop : -0.34 (0.28), residues: 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.1731 time to fit residues: 10.0252 Evaluate side-chains 34 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0737 time to fit residues: 1.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8239 Z= 0.225 Angle : 0.560 9.755 11149 Z= 0.270 Chirality : 0.039 0.136 1267 Planarity : 0.002 0.026 1424 Dihedral : 4.118 21.751 1105 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.23 % Allowed : 13.14 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1025 helix: 2.14 (0.29), residues: 331 sheet: -0.26 (0.40), residues: 165 loop : -0.26 (0.29), residues: 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1694 time to fit residues: 9.8918 Evaluate side-chains 33 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0733 time to fit residues: 1.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8239 Z= 0.145 Angle : 0.564 10.431 11149 Z= 0.265 Chirality : 0.039 0.138 1267 Planarity : 0.002 0.039 1424 Dihedral : 3.989 19.703 1105 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.23 % Allowed : 13.72 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1025 helix: 2.17 (0.29), residues: 331 sheet: -0.25 (0.40), residues: 162 loop : -0.29 (0.28), residues: 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.958 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.1743 time to fit residues: 9.5682 Evaluate side-chains 33 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0974 time to fit residues: 1.4556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8239 Z= 0.246 Angle : 0.574 9.545 11149 Z= 0.274 Chirality : 0.039 0.135 1267 Planarity : 0.002 0.021 1424 Dihedral : 4.078 22.531 1105 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.23 % Allowed : 13.95 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1025 helix: 2.20 (0.29), residues: 331 sheet: -0.10 (0.40), residues: 165 loop : -0.23 (0.29), residues: 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.989 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1798 time to fit residues: 10.1549 Evaluate side-chains 33 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0789 time to fit residues: 1.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.0470 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8239 Z= 0.174 Angle : 0.586 12.154 11149 Z= 0.272 Chirality : 0.039 0.139 1267 Planarity : 0.002 0.020 1424 Dihedral : 4.038 22.109 1105 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.12 % Allowed : 14.07 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1025 helix: 2.17 (0.29), residues: 331 sheet: -0.08 (0.41), residues: 165 loop : -0.25 (0.28), residues: 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.987 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1777 time to fit residues: 10.2692 Evaluate side-chains 32 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.0040 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 500 HIS ** 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 = 0.3252 r_free = 0.3252 target = 0.048279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040816 restraints weight = 70444.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041794 restraints weight = 31145.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.042440 restraints weight = 18564.769| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8239 Z= 0.140 Angle : 0.566 10.693 11149 Z= 0.264 Chirality : 0.039 0.140 1267 Planarity : 0.002 0.019 1424 Dihedral : 3.971 21.727 1105 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.12 % Allowed : 13.95 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1025 helix: 2.13 (0.29), residues: 331 sheet: -0.05 (0.41), residues: 165 loop : -0.27 (0.28), residues: 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.10 seconds wall clock time: 29 minutes 30.19 seconds (1770.19 seconds total)