Starting phenix.real_space_refine (version: dev) on Sat Feb 18 04:58:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/02_2023/7u2b_26311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/02_2023/7u2b_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_26311/02_2023/7u2b_26311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/02_2023/7u2b_26311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/02_2023/7u2b_26311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2b_26311/02_2023/7u2b_26311_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9 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: 4.57, per 1000 atoms: 0.62 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: 3.43 Conformation dependent library (CDL) restraints added in 931.8 milliseconds 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: 2.42 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: 2.04 Time building geometry restraints manager: 3.66 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: 4257 30.30 - 60.61: 161 60.61 - 90.91: 7 90.91 - 121.22: 1 121.22 - 151.52: 3 Dihedral angle restraints: 4429 sinusoidal: 2191 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 4426 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 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. 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: 0.250 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: 1.730 Check model and map are aligned: 0.110 Process input model: 24.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 14.981 151.523 2991 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 % 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 *********************** 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 : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.2375 time to fit residues: 71.0747 Evaluate side-chains 99 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0394 ------------------------------------------------------------------------------- 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: 0.5980 chunk 34 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7585 Z= 0.197 Angle : 0.625 9.140 10525 Z= 0.315 Chirality : 0.038 0.160 1204 Planarity : 0.005 0.064 1184 Dihedral : 11.463 156.556 1493 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 0.15 % 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: 1.65 (0.29), residues: 772 helix: 1.93 (0.29), residues: 289 sheet: 1.39 (0.50), residues: 99 loop : 0.47 (0.31), residues: 384 *********************** 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 180 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2063 time to fit residues: 48.8809 Evaluate side-chains 101 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0302 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 20 optimal weight: 0.0000 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7585 Z= 0.159 Angle : 0.550 6.392 10525 Z= 0.278 Chirality : 0.037 0.155 1204 Planarity : 0.005 0.044 1184 Dihedral : 11.321 159.665 1493 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.00 % 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: 1.45 (0.29), residues: 772 helix: 1.54 (0.30), residues: 290 sheet: 1.79 (0.50), residues: 92 loop : 0.41 (0.30), residues: 390 *********************** 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 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2112 time to fit residues: 41.9653 Evaluate side-chains 93 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0489 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7585 Z= 0.167 Angle : 0.546 6.358 10525 Z= 0.281 Chirality : 0.037 0.145 1204 Planarity : 0.005 0.044 1184 Dihedral : 11.363 165.043 1493 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.00 % 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: 1.13 (0.29), residues: 772 helix: 1.19 (0.31), residues: 289 sheet: 1.43 (0.48), residues: 92 loop : 0.37 (0.30), residues: 391 *********************** 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 147 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.801 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2036 time to fit residues: 39.6844 Evaluate side-chains 97 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1154 ------------------------------------------------------------------------------- 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: 0.6980 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7585 Z= 0.205 Angle : 0.554 6.443 10525 Z= 0.284 Chirality : 0.038 0.147 1204 Planarity : 0.004 0.027 1184 Dihedral : 11.542 176.191 1493 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.00 % 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: 0.99 (0.29), residues: 772 helix: 1.05 (0.32), residues: 282 sheet: 1.39 (0.48), residues: 93 loop : 0.31 (0.30), residues: 397 *********************** 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 127 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1782 time to fit residues: 31.4013 Evaluate side-chains 91 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9676 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 190 HIS ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 7585 Z= 0.158 Angle : 0.529 6.286 10525 Z= 0.271 Chirality : 0.037 0.153 1204 Planarity : 0.004 0.024 1184 Dihedral : 11.563 179.317 1493 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.00 % 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: 0.97 (0.29), residues: 772 helix: 1.04 (0.31), residues: 289 sheet: 1.52 (0.51), residues: 92 loop : 0.24 (0.29), residues: 391 *********************** 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 135 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.912 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1775 time to fit residues: 33.4943 Evaluate side-chains 94 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0254 ------------------------------------------------------------------------------- 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: 0.3980 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 49 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 438 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: 0.7074 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7585 Z= 0.148 Angle : 0.532 8.347 10525 Z= 0.274 Chirality : 0.037 0.166 1204 Planarity : 0.004 0.029 1184 Dihedral : 11.545 179.074 1493 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % 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: 0.80 (0.29), residues: 772 helix: 0.77 (0.31), residues: 296 sheet: 1.37 (0.50), residues: 92 loop : 0.26 (0.30), residues: 384 *********************** 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 135 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.904 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1952 time to fit residues: 35.8829 Evaluate side-chains 91 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0557 ------------------------------------------------------------------------------- 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: 0.0980 chunk 15 optimal weight: 0.0570 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7585 Z= 0.143 Angle : 0.540 7.689 10525 Z= 0.278 Chirality : 0.037 0.142 1204 Planarity : 0.004 0.030 1184 Dihedral : 11.509 177.369 1493 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.00 % 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: 0.83 (0.29), residues: 772 helix: 0.90 (0.31), residues: 296 sheet: 1.25 (0.51), residues: 92 loop : 0.22 (0.30), residues: 384 *********************** 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 135 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.803 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1962 time to fit residues: 35.8804 Evaluate side-chains 95 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9591 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** 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: 0.7088 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7585 Z= 0.164 Angle : 0.536 7.360 10525 Z= 0.275 Chirality : 0.037 0.144 1204 Planarity : 0.004 0.025 1184 Dihedral : 11.505 174.552 1493 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.00 % 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: 0.72 (0.30), residues: 772 helix: 0.81 (0.31), residues: 299 sheet: 1.18 (0.53), residues: 92 loop : 0.16 (0.30), residues: 381 *********************** 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 128 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.784 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1869 time to fit residues: 33.4205 Evaluate side-chains 91 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9839 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 0.0010 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN B 277 ASN ** B 375 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: 0.7185 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7585 Z= 0.277 Angle : 0.612 7.725 10525 Z= 0.316 Chirality : 0.040 0.162 1204 Planarity : 0.005 0.036 1184 Dihedral : 11.755 170.725 1493 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.15 % 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: 0.52 (0.29), residues: 772 helix: 0.72 (0.32), residues: 286 sheet: 0.92 (0.54), residues: 93 loop : 0.03 (0.30), residues: 393 ********************** 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 113 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.778 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1849 time to fit residues: 28.9834 Evaluate side-chains 87 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0250 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 347 HIS ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102684 restraints weight = 12026.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105059 restraints weight = 6814.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106513 restraints weight = 4540.855| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5102 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= 0.173 Angle : 0.570 8.465 10525 Z= 0.292 Chirality : 0.038 0.141 1204 Planarity : 0.004 0.037 1184 Dihedral : 11.757 170.892 1493 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.00 % 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: 0.53 (0.30), residues: 772 helix: 0.73 (0.32), residues: 286 sheet: 0.83 (0.53), residues: 93 loop : 0.06 (0.30), residues: 393 =============================================================================== Job complete usr+sys time: 1611.32 seconds wall clock time: 30 minutes 20.12 seconds (1820.12 seconds total)