Starting phenix.real_space_refine on Mon Mar 11 06:09:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/03_2024/7u2b_26311_updated.pdb" } resolution = 4.1 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: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 34 5.16 5 C 4408 2.51 5 N 1316 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ARG 415": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ASP 472": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7316 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1111 Classifications: {'RNA': 53} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 26} Link IDs: {'rna2p': 5, 'rna3p': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' A%rna2p_pur:plan2': 1, ' A%rna2p_pur:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2500 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3647 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.65 Number of scatterers: 7316 At special positions: 0 Unit cell: (70.15, 95.45, 126.5, 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 34 16.00 P 53 15.00 O 1505 8.00 N 1316 7.00 C 4408 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: 3.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 4 sheets defined 37.6% alpha, 14.1% beta 8 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 221 through 224 No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 361 through 382 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 479 through 485 removed outlier: 4.254A pdb=" N SER A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 60 through 63 No H-bonds generated for 'chain 'B' and resid 60 through 63' Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 83 through 122 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 133 through 169 Proline residue: B 154 - end of helix removed outlier: 4.311A pdb=" N LYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 361 through 382 Processing helix chain 'B' and resid 393 through 396 No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 479 through 485 removed outlier: 4.076A pdb=" N SER B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 256 through 258 removed outlier: 4.097A pdb=" N SER A 325 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 326 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 350 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 455 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET A 353 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR A 453 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY A 355 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASN A 451 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 357 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR A 449 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 449 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN A 451 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 453 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 421 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 402 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP A 390 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 188 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 407 through 410 removed outlier: 3.773A pdb=" N MET A 410 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 415 " --> pdb=" O MET A 410 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 256 through 258 removed outlier: 4.068A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 326 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 350 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 455 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET B 353 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR B 453 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY B 355 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN B 451 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 406 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER B 421 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 404 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 312 through 314 removed outlier: 7.360A pdb=" N MET B 436 " --> pdb=" O VAL B 313 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2090 1.33 - 1.45: 1486 1.45 - 1.57: 3841 1.57 - 1.69: 112 1.69 - 1.81: 56 Bond restraints: 7585 Sorted by residual: bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.519 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.731 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" O2S SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.435 1.584 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.581 -0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 7580 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 513 106.51 - 113.38: 4214 113.38 - 120.25: 2905 120.25 - 127.12: 2714 127.12 - 133.99: 179 Bond angle restraints: 10525 Sorted by residual: angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 101.24 20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 102.90 18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" N THR B 426 " pdb=" CA THR B 426 " pdb=" C THR B 426 " ideal model delta sigma weight residual 111.37 117.25 -5.88 1.64e+00 3.72e-01 1.28e+01 angle pdb=" N1 SSA B 601 " pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 119.38 108.72 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N VAL B 223 " pdb=" CA VAL B 223 " pdb=" C VAL B 223 " ideal model delta sigma weight residual 109.34 116.64 -7.30 2.08e+00 2.31e-01 1.23e+01 ... (remaining 10520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 4366 30.30 - 60.61: 225 60.61 - 90.91: 62 90.91 - 121.22: 1 121.22 - 151.52: 3 Dihedral angle restraints: 4657 sinusoidal: 2419 harmonic: 2238 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual -160.00 -8.48 -151.52 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sinusoidal sigma weight residual -160.00 -10.64 -149.36 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' C C 10 " pdb=" C1' C C 10 " pdb=" N1 C C 10 " pdb=" C2 C C 10 " ideal model delta sinusoidal sigma weight residual -160.00 -16.50 -143.50 1 1.50e+01 4.44e-03 7.70e+01 ... (remaining 4654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1170 0.113 - 0.226: 32 0.226 - 0.339: 0 0.339 - 0.453: 0 0.453 - 0.566: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA SSA B 601 " pdb=" CB SSA B 601 " pdb=" C9 SSA B 601 " pdb=" N10 SSA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.03 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA SSA A 601 " pdb=" CB SSA A 601 " pdb=" C9 SSA A 601 " pdb=" N10 SSA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.02 0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1201 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 45 " -0.030 2.00e-02 2.50e+03 1.43e-02 5.64e+00 pdb=" N9 A C 45 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A C 45 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 45 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A C 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A C 45 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 45 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 45 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C 45 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 45 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " -0.029 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 458 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 457 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 458 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.022 5.00e-02 4.00e+02 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 47 2.53 - 3.12: 5659 3.12 - 3.71: 11588 3.71 - 4.31: 15608 4.31 - 4.90: 25233 Nonbonded interactions: 58135 Sorted by model distance: nonbonded pdb=" O2 C C 8 " pdb=" O2' C C 33 " model vdw 1.936 2.440 nonbonded pdb=" O2' A C 45 " pdb=" O5' A C 46 " model vdw 2.011 2.440 nonbonded pdb=" OG1 THR A 453 " pdb=" OG SSA A 601 " model vdw 2.032 2.440 nonbonded pdb=" OG SER A 224 " pdb=" OG SER A 228 " model vdw 2.059 2.440 nonbonded pdb=" OH TYR A 329 " pdb=" OH TYR B 329 " model vdw 2.099 2.440 ... (remaining 58130 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.450 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.370 Find NCS groups from input model: 0.170 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.009 0.187 7585 Z= 0.626 Angle : 0.962 20.098 10525 Z= 0.520 Chirality : 0.051 0.566 1204 Planarity : 0.004 0.043 1184 Dihedral : 18.560 151.523 3219 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 12.52 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.29), residues: 772 helix: 3.12 (0.28), residues: 288 sheet: 0.78 (0.48), residues: 105 loop : 0.40 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 409 HIS 0.005 0.001 HIS A 240 PHE 0.022 0.002 PHE B 404 TYR 0.014 0.002 TYR B 230 ARG 0.010 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8547 (mtt) cc_final: 0.8124 (mmm) REVERT: A 205 HIS cc_start: 0.8447 (p-80) cc_final: 0.8172 (p-80) REVERT: A 211 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8225 (tmtt) REVERT: A 218 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7820 (mmmm) REVERT: A 258 MET cc_start: 0.8254 (ttm) cc_final: 0.7646 (mtp) REVERT: A 425 CYS cc_start: 0.8546 (m) cc_final: 0.8241 (t) REVERT: A 451 ASN cc_start: 0.8559 (p0) cc_final: 0.7950 (p0) REVERT: A 468 ASN cc_start: 0.8250 (m-40) cc_final: 0.7814 (m-40) REVERT: A 477 VAL cc_start: 0.8386 (t) cc_final: 0.8156 (p) REVERT: A 482 GLN cc_start: 0.8187 (mt0) cc_final: 0.7896 (pp30) REVERT: B 153 TYR cc_start: 0.8243 (m-80) cc_final: 0.7590 (m-80) REVERT: B 248 ASN cc_start: 0.7962 (m-40) cc_final: 0.7322 (t0) REVERT: B 252 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8546 (ttp-110) REVERT: B 256 THR cc_start: 0.7597 (m) cc_final: 0.6740 (p) REVERT: B 326 SER cc_start: 0.8804 (p) cc_final: 0.8521 (t) REVERT: B 366 GLN cc_start: 0.6857 (tt0) cc_final: 0.6395 (tm-30) REVERT: B 437 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6557 (p90) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.2296 time to fit residues: 68.8628 Evaluate side-chains 114 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 295 ASN A 451 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7585 Z= 0.257 Angle : 0.633 7.076 10525 Z= 0.322 Chirality : 0.039 0.163 1204 Planarity : 0.005 0.048 1184 Dihedral : 18.704 157.695 1721 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.31 % Allowed : 4.27 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 772 helix: 1.82 (0.29), residues: 289 sheet: 1.38 (0.49), residues: 97 loop : 0.35 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 93 HIS 0.007 0.001 HIS B 347 PHE 0.022 0.002 PHE B 247 TYR 0.036 0.003 TYR B 47 ARG 0.005 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8677 (mp0) cc_final: 0.8327 (tt0) REVERT: A 211 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8167 (tmtt) REVERT: A 218 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7818 (mmmt) REVERT: A 250 LEU cc_start: 0.9223 (mm) cc_final: 0.9015 (mt) REVERT: A 258 MET cc_start: 0.8166 (ttm) cc_final: 0.7583 (mtp) REVERT: A 264 LEU cc_start: 0.9048 (mm) cc_final: 0.8768 (mp) REVERT: A 287 ASP cc_start: 0.8761 (t0) cc_final: 0.8502 (t0) REVERT: A 449 THR cc_start: 0.8734 (p) cc_final: 0.8450 (p) REVERT: A 482 GLN cc_start: 0.8426 (mt0) cc_final: 0.7871 (pp30) REVERT: B 153 TYR cc_start: 0.8463 (m-80) cc_final: 0.7948 (m-80) REVERT: B 191 MET cc_start: 0.7056 (mtt) cc_final: 0.6647 (mtt) REVERT: B 248 ASN cc_start: 0.7990 (m-40) cc_final: 0.7375 (t0) REVERT: B 252 ARG cc_start: 0.8913 (tpp-160) cc_final: 0.8693 (ttm110) REVERT: B 326 SER cc_start: 0.8788 (p) cc_final: 0.8199 (t) REVERT: B 353 MET cc_start: 0.7539 (mtp) cc_final: 0.7055 (mtp) REVERT: B 366 GLN cc_start: 0.6874 (tt0) cc_final: 0.6377 (tm-30) REVERT: B 391 MET cc_start: 0.8521 (tpt) cc_final: 0.8312 (tmm) REVERT: B 395 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 401 TYR cc_start: 0.8807 (t80) cc_final: 0.8529 (t80) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.1932 time to fit residues: 43.2005 Evaluate side-chains 114 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.0170 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7585 Z= 0.197 Angle : 0.561 6.507 10525 Z= 0.287 Chirality : 0.038 0.148 1204 Planarity : 0.005 0.038 1184 Dihedral : 18.481 161.884 1721 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 772 helix: 1.36 (0.30), residues: 283 sheet: 1.64 (0.50), residues: 90 loop : 0.37 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 409 HIS 0.003 0.001 HIS B 190 PHE 0.010 0.001 PHE B 163 TYR 0.029 0.002 TYR A 329 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8642 (mtt) cc_final: 0.8340 (mmm) REVERT: A 207 GLU cc_start: 0.8648 (mp0) cc_final: 0.8333 (mp0) REVERT: A 211 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8171 (tptp) REVERT: A 218 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8074 (mmmt) REVERT: A 258 MET cc_start: 0.8212 (ttm) cc_final: 0.7530 (mtp) REVERT: A 287 ASP cc_start: 0.8570 (t0) cc_final: 0.8316 (t0) REVERT: A 293 ASP cc_start: 0.8635 (m-30) cc_final: 0.8298 (m-30) REVERT: A 367 LEU cc_start: 0.8736 (tp) cc_final: 0.8464 (tp) REVERT: A 468 ASN cc_start: 0.8129 (m-40) cc_final: 0.6772 (t0) REVERT: A 477 VAL cc_start: 0.8105 (t) cc_final: 0.7593 (p) REVERT: B 52 TYR cc_start: 0.8275 (m-10) cc_final: 0.7917 (m-10) REVERT: B 153 TYR cc_start: 0.8337 (m-80) cc_final: 0.7868 (m-80) REVERT: B 248 ASN cc_start: 0.7801 (m-40) cc_final: 0.7066 (t0) REVERT: B 252 ARG cc_start: 0.8820 (tpp-160) cc_final: 0.8510 (ttp-110) REVERT: B 326 SER cc_start: 0.8811 (p) cc_final: 0.8468 (p) REVERT: B 366 GLN cc_start: 0.6853 (tt0) cc_final: 0.6399 (tm-30) REVERT: B 391 MET cc_start: 0.8622 (tpt) cc_final: 0.8382 (mmm) REVERT: B 410 MET cc_start: 0.8477 (mpp) cc_final: 0.8160 (mpp) REVERT: B 451 ASN cc_start: 0.7987 (p0) cc_final: 0.7434 (p0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2114 time to fit residues: 44.6675 Evaluate side-chains 112 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7585 Z= 0.168 Angle : 0.539 6.448 10525 Z= 0.276 Chirality : 0.037 0.151 1204 Planarity : 0.004 0.047 1184 Dihedral : 18.361 166.905 1721 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 772 helix: 1.15 (0.31), residues: 290 sheet: 1.52 (0.50), residues: 90 loop : 0.38 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 409 HIS 0.003 0.001 HIS B 190 PHE 0.009 0.001 PHE B 308 TYR 0.033 0.002 TYR A 230 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8627 (mtt) cc_final: 0.7816 (mmm) REVERT: A 207 GLU cc_start: 0.8695 (mp0) cc_final: 0.8449 (mp0) REVERT: A 218 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8015 (mmmm) REVERT: A 258 MET cc_start: 0.8149 (ttm) cc_final: 0.7488 (mtp) REVERT: A 287 ASP cc_start: 0.8567 (t0) cc_final: 0.8306 (t0) REVERT: A 293 ASP cc_start: 0.8575 (m-30) cc_final: 0.8284 (m-30) REVERT: A 468 ASN cc_start: 0.8093 (m-40) cc_final: 0.6722 (t0) REVERT: A 477 VAL cc_start: 0.8128 (t) cc_final: 0.7466 (p) REVERT: B 52 TYR cc_start: 0.8181 (m-10) cc_final: 0.7910 (m-10) REVERT: B 153 TYR cc_start: 0.8263 (m-80) cc_final: 0.7750 (m-80) REVERT: B 248 ASN cc_start: 0.7878 (m-40) cc_final: 0.7273 (t0) REVERT: B 252 ARG cc_start: 0.8859 (tpp-160) cc_final: 0.8541 (ttp-110) REVERT: B 258 MET cc_start: 0.8413 (mtp) cc_final: 0.8209 (mtp) REVERT: B 326 SER cc_start: 0.8801 (p) cc_final: 0.8464 (p) REVERT: B 366 GLN cc_start: 0.6873 (tt0) cc_final: 0.6393 (tm-30) REVERT: B 410 MET cc_start: 0.8580 (mpp) cc_final: 0.8238 (mpp) REVERT: B 436 MET cc_start: 0.7654 (ttm) cc_final: 0.7314 (ttt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1893 time to fit residues: 39.3496 Evaluate side-chains 106 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS A 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7585 Z= 0.258 Angle : 0.583 6.670 10525 Z= 0.300 Chirality : 0.039 0.167 1204 Planarity : 0.005 0.038 1184 Dihedral : 18.413 176.297 1721 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.88 (0.29), residues: 772 helix: 1.01 (0.31), residues: 283 sheet: 1.30 (0.51), residues: 89 loop : 0.22 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 93 HIS 0.006 0.001 HIS B 190 PHE 0.016 0.002 PHE B 404 TYR 0.026 0.002 TYR A 230 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8588 (mtt) cc_final: 0.8220 (mmm) REVERT: A 207 GLU cc_start: 0.8873 (mp0) cc_final: 0.8536 (mp0) REVERT: A 218 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8151 (mmmt) REVERT: A 258 MET cc_start: 0.8293 (ttm) cc_final: 0.7610 (mtp) REVERT: A 287 ASP cc_start: 0.8623 (t0) cc_final: 0.8327 (t0) REVERT: A 443 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 468 ASN cc_start: 0.8352 (m-40) cc_final: 0.7133 (t0) REVERT: A 477 VAL cc_start: 0.8199 (t) cc_final: 0.7511 (p) REVERT: B 52 TYR cc_start: 0.8114 (m-10) cc_final: 0.7758 (m-10) REVERT: B 248 ASN cc_start: 0.7925 (m-40) cc_final: 0.7257 (t0) REVERT: B 252 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8566 (ttp-110) REVERT: B 258 MET cc_start: 0.8530 (mtp) cc_final: 0.8115 (mtp) REVERT: B 322 MET cc_start: 0.6824 (mtt) cc_final: 0.6435 (mtt) REVERT: B 366 GLN cc_start: 0.6977 (tt0) cc_final: 0.6488 (tm-30) REVERT: B 410 MET cc_start: 0.8674 (mpp) cc_final: 0.8319 (mpp) REVERT: B 436 MET cc_start: 0.7746 (ttm) cc_final: 0.7399 (ttt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1694 time to fit residues: 33.4983 Evaluate side-chains 99 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7585 Z= 0.166 Angle : 0.544 7.979 10525 Z= 0.280 Chirality : 0.038 0.148 1204 Planarity : 0.004 0.029 1184 Dihedral : 18.396 177.189 1721 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.84 (0.29), residues: 772 helix: 0.94 (0.31), residues: 290 sheet: 1.07 (0.51), residues: 92 loop : 0.28 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 93 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.001 PHE B 291 TYR 0.035 0.002 TYR A 230 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8612 (mtt) cc_final: 0.8270 (mmm) REVERT: A 207 GLU cc_start: 0.8819 (mp0) cc_final: 0.8515 (mp0) REVERT: A 218 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8185 (mmmt) REVERT: A 258 MET cc_start: 0.8327 (ttm) cc_final: 0.7606 (mtp) REVERT: A 287 ASP cc_start: 0.8621 (t0) cc_final: 0.8310 (t0) REVERT: A 293 ASP cc_start: 0.8483 (m-30) cc_final: 0.8104 (m-30) REVERT: A 468 ASN cc_start: 0.8449 (m-40) cc_final: 0.7121 (t0) REVERT: B 52 TYR cc_start: 0.8315 (m-10) cc_final: 0.7957 (m-10) REVERT: B 248 ASN cc_start: 0.7833 (m-40) cc_final: 0.7421 (t0) REVERT: B 252 ARG cc_start: 0.8882 (tpp-160) cc_final: 0.8677 (mtm-85) REVERT: B 262 ASP cc_start: 0.8125 (m-30) cc_final: 0.7830 (m-30) REVERT: B 366 GLN cc_start: 0.6878 (tt0) cc_final: 0.6375 (tm-30) REVERT: B 391 MET cc_start: 0.8732 (tpt) cc_final: 0.8332 (tmm) REVERT: B 410 MET cc_start: 0.8691 (mpp) cc_final: 0.8346 (mpp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1834 time to fit residues: 35.7034 Evaluate side-chains 108 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7585 Z= 0.186 Angle : 0.551 10.885 10525 Z= 0.281 Chirality : 0.038 0.145 1204 Planarity : 0.004 0.029 1184 Dihedral : 18.386 179.452 1721 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.82 (0.29), residues: 772 helix: 0.96 (0.32), residues: 286 sheet: 0.97 (0.51), residues: 92 loop : 0.25 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 93 HIS 0.006 0.001 HIS A 347 PHE 0.011 0.001 PHE B 163 TYR 0.015 0.002 TYR B 329 ARG 0.004 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8604 (mtt) cc_final: 0.8073 (mmm) REVERT: A 207 GLU cc_start: 0.8835 (mp0) cc_final: 0.8555 (mp0) REVERT: A 218 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8181 (mmmt) REVERT: A 221 SER cc_start: 0.8771 (m) cc_final: 0.8548 (t) REVERT: A 258 MET cc_start: 0.8302 (ttm) cc_final: 0.7417 (mtp) REVERT: A 287 ASP cc_start: 0.8644 (t0) cc_final: 0.8331 (t0) REVERT: A 468 ASN cc_start: 0.8380 (m-40) cc_final: 0.7001 (t0) REVERT: B 52 TYR cc_start: 0.8277 (m-10) cc_final: 0.7926 (m-10) REVERT: B 248 ASN cc_start: 0.7854 (m-40) cc_final: 0.7270 (t0) REVERT: B 252 ARG cc_start: 0.8932 (tpp-160) cc_final: 0.8726 (mtm-85) REVERT: B 366 GLN cc_start: 0.6928 (tt0) cc_final: 0.6429 (tm-30) REVERT: B 377 GLU cc_start: 0.8570 (tp30) cc_final: 0.8006 (tp30) REVERT: B 391 MET cc_start: 0.8773 (tpt) cc_final: 0.8397 (tmm) REVERT: B 410 MET cc_start: 0.8697 (mpp) cc_final: 0.8380 (mpp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1810 time to fit residues: 35.3765 Evaluate side-chains 110 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7585 Z= 0.149 Angle : 0.526 6.329 10525 Z= 0.272 Chirality : 0.038 0.234 1204 Planarity : 0.004 0.029 1184 Dihedral : 18.405 178.713 1721 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.86 (0.30), residues: 772 helix: 1.00 (0.32), residues: 292 sheet: 0.99 (0.51), residues: 92 loop : 0.27 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 93 HIS 0.008 0.001 HIS B 190 PHE 0.020 0.001 PHE B 291 TYR 0.026 0.001 TYR A 230 ARG 0.005 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8611 (mtt) cc_final: 0.8093 (mmm) REVERT: A 207 GLU cc_start: 0.8804 (mp0) cc_final: 0.8517 (mp0) REVERT: A 218 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8200 (mmmt) REVERT: A 221 SER cc_start: 0.8852 (m) cc_final: 0.8641 (t) REVERT: A 258 MET cc_start: 0.8364 (ttm) cc_final: 0.7575 (mtp) REVERT: A 287 ASP cc_start: 0.8610 (t0) cc_final: 0.8299 (t0) REVERT: A 293 ASP cc_start: 0.8397 (m-30) cc_final: 0.8109 (t70) REVERT: A 468 ASN cc_start: 0.8425 (m-40) cc_final: 0.7020 (t0) REVERT: B 248 ASN cc_start: 0.7711 (m-40) cc_final: 0.7167 (t0) REVERT: B 252 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8649 (mtm-85) REVERT: B 326 SER cc_start: 0.8720 (p) cc_final: 0.8255 (t) REVERT: B 347 HIS cc_start: 0.8609 (p-80) cc_final: 0.8267 (p-80) REVERT: B 366 GLN cc_start: 0.6930 (tt0) cc_final: 0.6419 (tm-30) REVERT: B 377 GLU cc_start: 0.8509 (tp30) cc_final: 0.7954 (tp30) REVERT: B 391 MET cc_start: 0.8650 (tpt) cc_final: 0.8258 (tmm) REVERT: B 410 MET cc_start: 0.8678 (mpp) cc_final: 0.8401 (mpp) REVERT: B 436 MET cc_start: 0.6756 (tmm) cc_final: 0.6367 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1677 time to fit residues: 31.2469 Evaluate side-chains 103 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7585 Z= 0.183 Angle : 0.550 7.362 10525 Z= 0.284 Chirality : 0.038 0.172 1204 Planarity : 0.004 0.028 1184 Dihedral : 18.351 176.934 1721 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.81 (0.30), residues: 772 helix: 0.96 (0.32), residues: 290 sheet: 1.20 (0.52), residues: 91 loop : 0.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.007 0.001 HIS B 190 PHE 0.029 0.002 PHE B 371 TYR 0.020 0.001 TYR A 230 ARG 0.003 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8614 (mtt) cc_final: 0.8090 (mmm) REVERT: A 200 PHE cc_start: 0.8391 (p90) cc_final: 0.7873 (p90) REVERT: A 207 GLU cc_start: 0.8811 (mp0) cc_final: 0.8520 (mp0) REVERT: A 218 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8205 (mmmt) REVERT: A 221 SER cc_start: 0.8880 (m) cc_final: 0.8660 (t) REVERT: A 258 MET cc_start: 0.8380 (ttm) cc_final: 0.7563 (mtp) REVERT: A 287 ASP cc_start: 0.8606 (t0) cc_final: 0.8303 (t0) REVERT: A 293 ASP cc_start: 0.8389 (m-30) cc_final: 0.8142 (t70) REVERT: A 468 ASN cc_start: 0.8471 (m-40) cc_final: 0.7055 (t0) REVERT: B 104 ARG cc_start: 0.6365 (tmm160) cc_final: 0.6066 (tmm160) REVERT: B 248 ASN cc_start: 0.7715 (m-40) cc_final: 0.7207 (t0) REVERT: B 252 ARG cc_start: 0.8842 (tpp-160) cc_final: 0.8524 (mtm-85) REVERT: B 326 SER cc_start: 0.8709 (p) cc_final: 0.8274 (t) REVERT: B 347 HIS cc_start: 0.8621 (p-80) cc_final: 0.8309 (p-80) REVERT: B 366 GLN cc_start: 0.6931 (tt0) cc_final: 0.6455 (tm-30) REVERT: B 377 GLU cc_start: 0.8519 (tp30) cc_final: 0.7971 (tp30) REVERT: B 391 MET cc_start: 0.8736 (tpt) cc_final: 0.8117 (tmm) REVERT: B 410 MET cc_start: 0.8681 (mpp) cc_final: 0.8387 (mpp) REVERT: B 436 MET cc_start: 0.6834 (tmm) cc_final: 0.6410 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1653 time to fit residues: 30.5020 Evaluate side-chains 100 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.0030 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7585 Z= 0.153 Angle : 0.535 7.181 10525 Z= 0.275 Chirality : 0.038 0.146 1204 Planarity : 0.004 0.029 1184 Dihedral : 18.277 175.653 1721 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.30), residues: 772 helix: 0.97 (0.32), residues: 293 sheet: 0.98 (0.50), residues: 95 loop : 0.27 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 409 HIS 0.007 0.001 HIS B 190 PHE 0.033 0.002 PHE B 371 TYR 0.013 0.001 TYR B 164 ARG 0.004 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8594 (mtt) cc_final: 0.8088 (mmm) REVERT: A 200 PHE cc_start: 0.8388 (p90) cc_final: 0.7831 (p90) REVERT: A 207 GLU cc_start: 0.8811 (mp0) cc_final: 0.8512 (mp0) REVERT: A 218 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8217 (mmmt) REVERT: A 221 SER cc_start: 0.8882 (m) cc_final: 0.8672 (t) REVERT: A 258 MET cc_start: 0.8384 (ttm) cc_final: 0.7439 (mtp) REVERT: A 287 ASP cc_start: 0.8620 (t0) cc_final: 0.8327 (t0) REVERT: A 293 ASP cc_start: 0.8411 (m-30) cc_final: 0.8097 (t70) REVERT: A 468 ASN cc_start: 0.8439 (m-40) cc_final: 0.7073 (t0) REVERT: B 104 ARG cc_start: 0.6359 (tmm160) cc_final: 0.6043 (tmm160) REVERT: B 252 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8572 (mtm-85) REVERT: B 321 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7514 (ptp-170) REVERT: B 326 SER cc_start: 0.8663 (p) cc_final: 0.8244 (t) REVERT: B 347 HIS cc_start: 0.8621 (p-80) cc_final: 0.8352 (p-80) REVERT: B 366 GLN cc_start: 0.6924 (tt0) cc_final: 0.6454 (tm-30) REVERT: B 391 MET cc_start: 0.8619 (tpt) cc_final: 0.7971 (tmm) REVERT: B 410 MET cc_start: 0.8661 (mpp) cc_final: 0.8402 (mpp) REVERT: B 436 MET cc_start: 0.6732 (tmm) cc_final: 0.6024 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1825 time to fit residues: 33.3382 Evaluate side-chains 101 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106019 restraints weight = 11636.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108494 restraints weight = 6690.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110143 restraints weight = 4499.105| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7585 Z= 0.148 Angle : 0.517 6.357 10525 Z= 0.269 Chirality : 0.037 0.146 1204 Planarity : 0.004 0.030 1184 Dihedral : 18.241 173.930 1721 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.30), residues: 772 helix: 0.97 (0.32), residues: 292 sheet: 1.00 (0.50), residues: 96 loop : 0.26 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 409 HIS 0.007 0.001 HIS B 190 PHE 0.032 0.002 PHE A 255 TYR 0.010 0.001 TYR A 401 ARG 0.003 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.75 seconds wall clock time: 31 minutes 17.28 seconds (1877.28 seconds total)