Starting phenix.real_space_refine on Wed Feb 14 20:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/02_2024/6x68_22073.pdb" } resolution = 3.66 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 124 5.49 5 S 88 5.16 5 C 6063 2.51 5 N 1811 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "D" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "A" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1517 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1025 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3568 SG CYS C 559 43.876 58.830 53.085 1.00101.37 S ATOM 3593 SG CYS C 562 44.008 62.320 53.323 1.00101.18 S ATOM 3747 SG CYS C 582 44.083 60.658 50.274 1.00102.93 S ATOM 3684 SG CYS C 574 50.264 50.434 49.266 1.00157.97 S ATOM 3708 SG CYS C 577 50.090 49.390 52.178 1.00145.09 S ATOM 3815 SG CYS C 590 51.546 52.352 51.479 1.00159.91 S ATOM 3836 SG CYS C 593 52.626 49.806 51.000 1.00172.88 S ATOM 7416 SG CYS D 559 50.389 56.078 28.512 1.00 0.00 S ATOM 7441 SG CYS D 562 47.844 55.761 27.137 1.00319.64 S ATOM 7595 SG CYS D 582 47.770 55.742 30.601 1.00289.96 S ATOM 7532 SG CYS D 574 58.188 55.339 37.702 1.00325.15 S ATOM 7556 SG CYS D 577 60.281 55.493 35.331 1.00356.83 S ATOM 7663 SG CYS D 590 58.020 52.711 36.125 1.00303.36 S ATOM 7684 SG CYS D 593 59.976 53.297 37.650 1.00322.51 S Time building chain proxies: 5.95, per 1000 atoms: 0.58 Number of scatterers: 10246 At special positions: 0 Unit cell: (95.04, 90.72, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 88 16.00 P 124 15.00 O 2152 8.00 N 1811 7.00 C 6063 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: 4.43 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 582 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 559 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 585 " pdb=" ZN C 604 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 577 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 593 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 590 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 574 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 562 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 582 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 559 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 585 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 593 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 590 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 577 " Number of angles added : 18 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 46.1% alpha, 11.5% beta 52 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.935A pdb=" N PHE C 138 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU C 142 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 172 through 189 Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.838A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.611A pdb=" N LEU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 443 through 453 removed outlier: 4.831A pdb=" N ASP C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 491 removed outlier: 4.055A pdb=" N LEU C 469 " --> pdb=" O TRP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 519 removed outlier: 3.680A pdb=" N SER C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 519 " --> pdb=" O MET C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.075A pdb=" N ALA D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 172 through 190 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 244 through 257 removed outlier: 3.744A pdb=" N GLN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 337 Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.885A pdb=" N THR D 350 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 433 through 443 removed outlier: 3.948A pdb=" N GLN D 441 " --> pdb=" O MET D 437 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 442 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 464 through 491 removed outlier: 3.542A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 470 " --> pdb=" O PRO D 466 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 482 " --> pdb=" O CYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 5.383A pdb=" N SER D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 519 " --> pdb=" O MET D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 590 through 594 Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.828A pdb=" N MET C 298 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY C 309 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 296 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS C 294 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 265 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 574 removed outlier: 3.539A pdb=" N LYS C 579 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.457A pdb=" N ASP D 300 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET D 306 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 283 removed outlier: 5.029A pdb=" N ILE D 367 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 572 through 573 332 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2084 1.33 - 1.45: 3323 1.45 - 1.58: 4912 1.58 - 1.71: 247 1.71 - 1.83: 136 Bond restraints: 10702 Sorted by residual: bond pdb=" O3' DA A 33 " pdb=" P DT A 34 " ideal model delta sigma weight residual 1.607 1.516 0.091 1.50e-02 4.44e+03 3.72e+01 bond pdb=" N SER D 289 " pdb=" CA SER D 289 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.19e-02 7.06e+03 3.10e+01 bond pdb=" N ASN C 384 " pdb=" CA ASN C 384 " ideal model delta sigma weight residual 1.454 1.392 0.061 1.23e-02 6.61e+03 2.47e+01 bond pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.21e-02 6.83e+03 2.33e+01 bond pdb=" C4' DT A 34 " pdb=" C3' DT A 34 " ideal model delta sigma weight residual 1.523 1.617 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 10697 not shown) Histogram of bond angle deviations from ideal: 90.81 - 100.23: 16 100.23 - 109.64: 2855 109.64 - 119.06: 6629 119.06 - 128.47: 5301 128.47 - 137.89: 169 Bond angle restraints: 14970 Sorted by residual: angle pdb=" CA ASN C 384 " pdb=" C ASN C 384 " pdb=" N SER C 385 " ideal model delta sigma weight residual 115.36 93.39 21.97 1.56e+00 4.11e-01 1.98e+02 angle pdb=" N VAL C 552 " pdb=" CA VAL C 552 " pdb=" C VAL C 552 " ideal model delta sigma weight residual 113.47 101.80 11.67 1.01e+00 9.80e-01 1.33e+02 angle pdb=" N ASN C 384 " pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 109.85 125.80 -15.95 1.58e+00 4.01e-01 1.02e+02 angle pdb=" CA ASN C 384 " pdb=" C ASN C 384 " pdb=" O ASN C 384 " ideal model delta sigma weight residual 121.46 132.88 -11.42 1.17e+00 7.31e-01 9.53e+01 angle pdb=" CA ARG D 315 " pdb=" C ARG D 315 " pdb=" N GLY D 316 " ideal model delta sigma weight residual 116.84 100.98 15.86 1.71e+00 3.42e-01 8.60e+01 ... (remaining 14965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 5681 33.95 - 67.90: 571 67.90 - 101.85: 6 101.85 - 135.80: 0 135.80 - 169.75: 2 Dihedral angle restraints: 6260 sinusoidal: 3444 harmonic: 2816 Sorted by residual: dihedral pdb=" C PRO D 408 " pdb=" N PRO D 408 " pdb=" CA PRO D 408 " pdb=" CB PRO D 408 " ideal model delta harmonic sigma weight residual -120.70 -107.37 -13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" C TYR D 527 " pdb=" N TYR D 527 " pdb=" CA TYR D 527 " pdb=" CB TYR D 527 " ideal model delta harmonic sigma weight residual -122.60 -110.50 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO C 541 " pdb=" N PRO C 541 " pdb=" CA PRO C 541 " pdb=" CB PRO C 541 " ideal model delta harmonic sigma weight residual -120.70 -108.72 -11.98 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 6257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1311 0.098 - 0.196: 290 0.196 - 0.294: 44 0.294 - 0.393: 10 0.393 - 0.491: 3 Chirality restraints: 1658 Sorted by residual: chirality pdb=" CA ASN C 384 " pdb=" N ASN C 384 " pdb=" C ASN C 384 " pdb=" CB ASN C 384 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PRO D 551 " pdb=" N PRO D 551 " pdb=" C PRO D 551 " pdb=" CB PRO D 551 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO D 410 " pdb=" N PRO D 410 " pdb=" C PRO D 410 " pdb=" CB PRO D 410 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1655 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 594 " -0.034 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE D 594 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE D 594 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE D 594 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 594 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C PHE C 594 " 0.100 2.00e-02 2.50e+03 pdb=" O PHE C 594 " -0.035 2.00e-02 2.50e+03 pdb=" OXT PHE C 594 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 507 " -0.061 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR D 507 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 507 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 507 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR D 507 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 507 " -0.046 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 9 2.30 - 2.95: 4458 2.95 - 3.60: 13893 3.60 - 4.25: 25472 4.25 - 4.90: 37684 Nonbonded interactions: 81516 Sorted by model distance: nonbonded pdb=" OP1 DT A -3 " pdb="CA CA A 101 " model vdw 1.652 2.510 nonbonded pdb=" OD2 ASP D 346 " pdb="CA CA A 101 " model vdw 1.905 2.510 nonbonded pdb=" OD2 ASP C 218 " pdb="CA CA C 602 " model vdw 2.030 2.510 nonbonded pdb=" OD2 ASP C 346 " pdb="CA CA C 601 " model vdw 2.075 2.510 nonbonded pdb=" OP1 DT B -3 " pdb="CA CA C 601 " model vdw 2.105 2.510 ... (remaining 81511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 117 through 594 or resid 601 or resid 603)) selection = (chain 'D' and (resid 117 through 594 or resid 601 or resid 603)) } 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: 0.290 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: 2.130 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.860 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.012 0.094 10702 Z= 0.746 Angle : 1.744 21.974 14970 Z= 1.196 Chirality : 0.087 0.491 1658 Planarity : 0.005 0.066 1472 Dihedral : 21.014 169.750 4440 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.52 % Favored : 97.16 % Rotamer: Outliers : 0.57 % Allowed : 6.90 % Favored : 92.53 % Cbeta Deviations : 1.10 % 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: -0.38 (0.26), residues: 952 helix: -1.14 (0.24), residues: 366 sheet: 1.50 (0.50), residues: 108 loop : 0.25 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.009 TRP C 465 HIS 0.009 0.003 HIS C 585 PHE 0.031 0.006 PHE D 349 TYR 0.061 0.010 TYR D 507 ARG 0.006 0.001 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 354 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 191 ASP cc_start: 0.7915 (p0) cc_final: 0.7481 (p0) REVERT: C 228 ASP cc_start: 0.7858 (t0) cc_final: 0.7625 (t70) REVERT: C 413 MET cc_start: 0.6567 (mpp) cc_final: 0.6333 (mpp) REVERT: C 462 THR cc_start: 0.7971 (t) cc_final: 0.7696 (p) REVERT: D 206 MET cc_start: 0.8437 (mmm) cc_final: 0.8207 (mmt) outliers start: 5 outliers final: 1 residues processed: 357 average time/residue: 0.2661 time to fit residues: 125.4426 Evaluate side-chains 224 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 ASN C 440 ASN C 441 GLN C 571 ASN D 253 HIS D 264 HIS D 347 ASN D 538 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10702 Z= 0.256 Angle : 0.780 8.649 14970 Z= 0.435 Chirality : 0.044 0.170 1658 Planarity : 0.005 0.044 1472 Dihedral : 24.411 161.959 2456 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.85 % Allowed : 17.42 % Favored : 78.73 % 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: 0.38 (0.28), residues: 952 helix: 0.41 (0.27), residues: 362 sheet: 1.36 (0.50), residues: 111 loop : -0.02 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 150 HIS 0.003 0.001 HIS D 585 PHE 0.036 0.002 PHE C 241 TYR 0.018 0.002 TYR D 439 ARG 0.007 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 LYS cc_start: 0.8650 (tppp) cc_final: 0.8283 (ttmm) REVERT: C 413 MET cc_start: 0.6285 (mpp) cc_final: 0.5977 (mpp) REVERT: C 565 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7850 (mmtp) REVERT: D 225 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7355 (mpt180) REVERT: D 267 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8098 (mt) REVERT: D 332 LEU cc_start: 0.7402 (mm) cc_final: 0.7010 (mm) REVERT: D 366 THR cc_start: 0.8092 (p) cc_final: 0.7831 (p) REVERT: D 536 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7843 (tp) outliers start: 34 outliers final: 18 residues processed: 273 average time/residue: 0.2354 time to fit residues: 88.2208 Evaluate side-chains 232 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN D 434 GLN D 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10702 Z= 0.251 Angle : 0.711 6.458 14970 Z= 0.398 Chirality : 0.042 0.161 1658 Planarity : 0.005 0.046 1472 Dihedral : 24.635 159.635 2454 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 4.64 % Allowed : 17.87 % Favored : 77.49 % 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: 0.44 (0.28), residues: 952 helix: 1.03 (0.29), residues: 354 sheet: 1.09 (0.52), residues: 110 loop : -0.40 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 465 HIS 0.002 0.001 HIS D 253 PHE 0.018 0.002 PHE D 349 TYR 0.014 0.001 TYR D 177 ARG 0.006 0.000 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: C 137 LEU cc_start: 0.8813 (tp) cc_final: 0.8588 (mp) REVERT: C 287 LYS cc_start: 0.8716 (tppp) cc_final: 0.8330 (ttmm) REVERT: C 356 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8622 (mtmm) REVERT: C 413 MET cc_start: 0.6034 (mpp) cc_final: 0.5826 (mpp) REVERT: C 565 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8189 (mmtp) REVERT: D 191 ASP cc_start: 0.8515 (p0) cc_final: 0.8263 (p0) REVERT: D 264 HIS cc_start: 0.7994 (m-70) cc_final: 0.7768 (m90) REVERT: D 332 LEU cc_start: 0.7671 (mm) cc_final: 0.7239 (mm) REVERT: D 536 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7817 (tp) REVERT: D 569 LYS cc_start: 0.5469 (mttt) cc_final: 0.4677 (tmtt) REVERT: D 589 MET cc_start: 0.7319 (mtp) cc_final: 0.7009 (mtt) outliers start: 41 outliers final: 27 residues processed: 252 average time/residue: 0.2120 time to fit residues: 75.6389 Evaluate side-chains 238 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 27 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN D 254 GLN D 347 ASN D 463 ASN D 488 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10702 Z= 0.236 Angle : 0.687 6.233 14970 Z= 0.381 Chirality : 0.041 0.145 1658 Planarity : 0.005 0.072 1472 Dihedral : 24.389 161.535 2454 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 4.75 % Allowed : 20.81 % Favored : 74.43 % 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: 0.33 (0.28), residues: 952 helix: 1.12 (0.29), residues: 356 sheet: 0.85 (0.50), residues: 115 loop : -0.60 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 348 HIS 0.001 0.000 HIS C 193 PHE 0.042 0.002 PHE C 241 TYR 0.011 0.001 TYR D 363 ARG 0.008 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 287 LYS cc_start: 0.8756 (tppp) cc_final: 0.8443 (ttmm) REVERT: C 356 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8308 (mtmm) REVERT: C 413 MET cc_start: 0.5908 (mpp) cc_final: 0.5617 (mpp) REVERT: C 565 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8241 (mmtp) REVERT: D 191 ASP cc_start: 0.8465 (p0) cc_final: 0.8070 (p0) REVERT: D 297 MET cc_start: 0.8358 (ttm) cc_final: 0.7986 (mtp) REVERT: D 332 LEU cc_start: 0.7632 (mm) cc_final: 0.7286 (mm) REVERT: D 536 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7893 (tp) REVERT: D 569 LYS cc_start: 0.5374 (mttt) cc_final: 0.4696 (tmtt) outliers start: 42 outliers final: 33 residues processed: 237 average time/residue: 0.2150 time to fit residues: 71.7862 Evaluate side-chains 234 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 536 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.0170 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN D 254 GLN D 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10702 Z= 0.212 Angle : 0.664 9.575 14970 Z= 0.365 Chirality : 0.040 0.153 1658 Planarity : 0.005 0.051 1472 Dihedral : 24.372 160.478 2454 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 4.30 % Allowed : 21.27 % Favored : 74.43 % 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: 0.38 (0.28), residues: 952 helix: 1.33 (0.29), residues: 354 sheet: 0.76 (0.50), residues: 115 loop : -0.68 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 348 HIS 0.002 0.001 HIS D 264 PHE 0.024 0.001 PHE C 241 TYR 0.011 0.001 TYR D 561 ARG 0.007 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: C 287 LYS cc_start: 0.8747 (tppp) cc_final: 0.8461 (ttmm) REVERT: C 356 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8369 (mtmm) REVERT: C 413 MET cc_start: 0.5948 (mpp) cc_final: 0.5445 (mpp) REVERT: C 565 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8181 (mmtp) REVERT: C 589 MET cc_start: 0.8145 (mpt) cc_final: 0.7446 (mpt) REVERT: D 264 HIS cc_start: 0.7925 (m-70) cc_final: 0.7676 (m-70) REVERT: D 297 MET cc_start: 0.8378 (ttm) cc_final: 0.8045 (mtp) REVERT: D 332 LEU cc_start: 0.7635 (mm) cc_final: 0.7383 (mm) REVERT: D 370 THR cc_start: 0.8149 (p) cc_final: 0.7713 (p) REVERT: D 536 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7958 (tp) REVERT: D 569 LYS cc_start: 0.5349 (mttt) cc_final: 0.4728 (tmtt) outliers start: 38 outliers final: 31 residues processed: 229 average time/residue: 0.1983 time to fit residues: 65.3712 Evaluate side-chains 229 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 587 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10702 Z= 0.353 Angle : 0.751 7.899 14970 Z= 0.413 Chirality : 0.043 0.142 1658 Planarity : 0.006 0.055 1472 Dihedral : 24.673 162.871 2454 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.77 % Allowed : 20.81 % Favored : 73.42 % 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: -0.05 (0.28), residues: 952 helix: 1.05 (0.28), residues: 363 sheet: 0.59 (0.50), residues: 115 loop : -1.07 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 465 HIS 0.003 0.001 HIS C 585 PHE 0.026 0.002 PHE C 241 TYR 0.016 0.002 TYR C 527 ARG 0.010 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: C 287 LYS cc_start: 0.8842 (tppp) cc_final: 0.8610 (ttmm) REVERT: C 356 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8392 (mtmm) REVERT: C 413 MET cc_start: 0.5782 (mpp) cc_final: 0.5272 (mpp) REVERT: C 454 SER cc_start: 0.8756 (t) cc_final: 0.8436 (t) REVERT: C 565 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8286 (mmtp) REVERT: C 589 MET cc_start: 0.8298 (mpt) cc_final: 0.8066 (mpt) REVERT: D 264 HIS cc_start: 0.8037 (m-70) cc_final: 0.7746 (m-70) REVERT: D 297 MET cc_start: 0.8394 (ttm) cc_final: 0.8025 (mtp) REVERT: D 382 LEU cc_start: 0.7628 (mp) cc_final: 0.7295 (mp) REVERT: D 536 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8088 (tp) REVERT: D 583 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.5053 (ptm160) outliers start: 51 outliers final: 39 residues processed: 226 average time/residue: 0.1983 time to fit residues: 64.3484 Evaluate side-chains 231 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10702 Z= 0.259 Angle : 0.709 12.573 14970 Z= 0.384 Chirality : 0.041 0.164 1658 Planarity : 0.005 0.060 1472 Dihedral : 24.587 159.167 2454 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.98 % Allowed : 21.61 % Favored : 73.42 % 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: -0.04 (0.28), residues: 952 helix: 1.22 (0.29), residues: 357 sheet: 0.54 (0.51), residues: 114 loop : -1.15 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 465 HIS 0.002 0.001 HIS C 585 PHE 0.020 0.002 PHE C 241 TYR 0.012 0.001 TYR D 561 ARG 0.006 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 0.986 Fit side-chains REVERT: C 356 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8380 (mtmm) REVERT: C 413 MET cc_start: 0.5747 (mpp) cc_final: 0.5200 (mpp) REVERT: C 454 SER cc_start: 0.8677 (t) cc_final: 0.8393 (t) REVERT: C 565 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8231 (mmtp) REVERT: D 264 HIS cc_start: 0.8050 (m-70) cc_final: 0.7761 (m-70) REVERT: D 297 MET cc_start: 0.8372 (ttm) cc_final: 0.7935 (mtp) REVERT: D 374 ASN cc_start: 0.7921 (p0) cc_final: 0.7515 (t0) REVERT: D 394 MET cc_start: 0.7145 (pmm) cc_final: 0.6934 (ptt) REVERT: D 456 MET cc_start: 0.8103 (mmm) cc_final: 0.7656 (mtp) REVERT: D 536 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8082 (tp) REVERT: D 583 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5063 (ptm160) outliers start: 44 outliers final: 32 residues processed: 221 average time/residue: 0.2081 time to fit residues: 65.8871 Evaluate side-chains 232 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 587 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10702 Z= 0.219 Angle : 0.689 13.451 14970 Z= 0.370 Chirality : 0.040 0.181 1658 Planarity : 0.005 0.062 1472 Dihedral : 24.485 157.967 2454 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.52 % Allowed : 22.74 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 952 helix: 1.42 (0.29), residues: 355 sheet: 0.48 (0.51), residues: 114 loop : -1.16 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 348 HIS 0.002 0.001 HIS C 585 PHE 0.018 0.001 PHE C 241 TYR 0.016 0.001 TYR C 312 ARG 0.004 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 0.911 Fit side-chains REVERT: C 138 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8089 (t80) REVERT: C 356 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8392 (mtmm) REVERT: C 413 MET cc_start: 0.5708 (mpp) cc_final: 0.5191 (mpp) REVERT: C 565 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8160 (mmtp) REVERT: D 264 HIS cc_start: 0.8005 (m-70) cc_final: 0.7689 (m-70) REVERT: D 297 MET cc_start: 0.8324 (ttm) cc_final: 0.7896 (mtp) REVERT: D 394 MET cc_start: 0.7102 (pmm) cc_final: 0.6897 (ptt) REVERT: D 456 MET cc_start: 0.8133 (mmm) cc_final: 0.7732 (mtp) REVERT: D 536 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8050 (tp) REVERT: D 583 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5121 (ptm160) outliers start: 40 outliers final: 33 residues processed: 224 average time/residue: 0.2092 time to fit residues: 67.3327 Evaluate side-chains 233 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 587 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.0270 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10702 Z= 0.304 Angle : 0.738 10.465 14970 Z= 0.396 Chirality : 0.042 0.157 1658 Planarity : 0.006 0.064 1472 Dihedral : 24.521 158.326 2454 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.75 % Allowed : 22.96 % Favored : 72.29 % 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: -0.24 (0.27), residues: 952 helix: 1.20 (0.29), residues: 366 sheet: 0.31 (0.52), residues: 110 loop : -1.40 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 465 HIS 0.004 0.001 HIS C 585 PHE 0.021 0.002 PHE D 349 TYR 0.018 0.002 TYR C 439 ARG 0.006 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 0.941 Fit side-chains REVERT: C 138 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8126 (t80) REVERT: C 356 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8405 (mtmm) REVERT: C 565 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8185 (mmtp) REVERT: D 297 MET cc_start: 0.8378 (ttm) cc_final: 0.7834 (mtp) REVERT: D 374 ASN cc_start: 0.7866 (p0) cc_final: 0.7465 (t0) REVERT: D 456 MET cc_start: 0.8090 (mmm) cc_final: 0.7682 (mtp) REVERT: D 536 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8013 (tp) REVERT: D 583 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5252 (ptm160) outliers start: 42 outliers final: 35 residues processed: 226 average time/residue: 0.1969 time to fit residues: 63.9974 Evaluate side-chains 239 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 583 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10702 Z= 0.278 Angle : 0.732 12.397 14970 Z= 0.388 Chirality : 0.041 0.152 1658 Planarity : 0.006 0.064 1472 Dihedral : 24.470 156.627 2454 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.52 % Allowed : 23.30 % Favored : 72.17 % 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: -0.16 (0.28), residues: 952 helix: 1.34 (0.29), residues: 357 sheet: 0.30 (0.52), residues: 110 loop : -1.36 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 465 HIS 0.003 0.001 HIS C 585 PHE 0.019 0.002 PHE C 241 TYR 0.027 0.002 TYR C 439 ARG 0.005 0.000 ARG D 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 1.107 Fit side-chains REVERT: C 138 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 356 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: C 565 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8219 (mmtp) REVERT: D 124 MET cc_start: 0.6794 (mmp) cc_final: 0.6195 (mmt) REVERT: D 169 ARG cc_start: 0.7493 (ptp90) cc_final: 0.7269 (ptp-110) REVERT: D 297 MET cc_start: 0.8220 (ttm) cc_final: 0.7706 (mtp) REVERT: D 374 ASN cc_start: 0.7846 (p0) cc_final: 0.7452 (t0) REVERT: D 456 MET cc_start: 0.8105 (mmm) cc_final: 0.7706 (mtp) REVERT: D 583 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.5237 (ptm160) outliers start: 40 outliers final: 34 residues processed: 222 average time/residue: 0.2105 time to fit residues: 66.5180 Evaluate side-chains 232 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 255 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 453 CYS Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 TYR Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 583 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106553 restraints weight = 18756.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110262 restraints weight = 8564.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112592 restraints weight = 5420.543| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10702 Z= 0.221 Angle : 0.703 12.192 14970 Z= 0.372 Chirality : 0.040 0.146 1658 Planarity : 0.005 0.063 1472 Dihedral : 24.374 155.063 2454 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.19 % Allowed : 23.64 % Favored : 72.17 % 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: -0.04 (0.28), residues: 952 helix: 1.43 (0.29), residues: 358 sheet: 0.53 (0.53), residues: 111 loop : -1.35 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 465 HIS 0.002 0.001 HIS C 585 PHE 0.019 0.001 PHE C 241 TYR 0.025 0.001 TYR C 439 ARG 0.005 0.000 ARG D 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.56 seconds wall clock time: 39 minutes 47.14 seconds (2387.14 seconds total)