Starting phenix.real_space_refine on Sun Mar 10 23:05:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0b_24102/03_2024/7n0b_24102.pdb" } resolution = 3.9 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= 0.003 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 P 39 5.49 5 S 52 5.16 5 C 3589 2.51 5 N 995 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5875 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4089 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "T" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 419 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 36.388 29.677 93.960 1.00 45.58 S ATOM 546 SG CYS A 77 33.521 31.561 95.217 1.00 35.44 S ATOM 651 SG CYS A 90 33.777 28.393 95.952 1.00 53.66 S ATOM 854 SG CYS A 117 44.933 12.952 101.734 1.00 87.14 S ATOM 874 SG CYS A 120 45.542 13.925 105.225 1.00 89.83 S ATOM 935 SG CYS A 128 48.215 13.881 102.415 1.00 79.86 S ATOM 947 SG CYS A 130 47.587 11.036 103.195 1.00 83.52 S ATOM 2581 SG CYS B 207 37.217 26.751 62.636 1.00 32.38 S ATOM 2601 SG CYS B 210 38.310 26.605 59.183 1.00 42.28 S ATOM 2722 SG CYS B 226 35.594 28.831 60.379 1.00 33.72 S ATOM 3022 SG CYS B 261 27.187 61.749 57.555 1.00 44.79 S ATOM 3152 SG CYS B 279 30.047 59.367 59.050 1.00 18.04 S ATOM 4542 SG CYS B 452 42.808 40.337 10.665 1.00 95.65 S ATOM 4698 SG CYS B 484 41.023 39.224 13.041 1.00 96.43 S Time building chain proxies: 3.95, per 1000 atoms: 0.67 Number of scatterers: 5875 At special positions: 0 Unit cell: (69.42, 91.848, 129.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 52 16.00 P 39 15.00 O 1193 8.00 N 995 7.00 C 3589 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " Number of angles added : 13 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1202 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 26.1% alpha, 12.0% beta 18 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.876A pdb=" N PHE A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.586A pdb=" N ALA A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.219A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 107 through 114 removed outlier: 4.029A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.526A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.893A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.863A pdb=" N MET B 276 " --> pdb=" O CYS B 272 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.596A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.934A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.725A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 removed outlier: 4.344A pdb=" N ASN B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.546A pdb=" N LEU B 519 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.256A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.648A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.712A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.721A pdb=" N LEU B 329 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 349 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.220A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 127 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.67 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: 1589 1.33 - 1.46: 1648 1.46 - 1.58: 2720 1.58 - 1.70: 76 1.70 - 1.83: 68 Bond restraints: 6101 Sorted by residual: bond pdb=" N ARG B 212 " pdb=" CA ARG B 212 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.31e-02 5.83e+03 9.96e+00 bond pdb=" ND1 HIS B 487 " pdb=" CE1 HIS B 487 " ideal model delta sigma weight residual 1.321 1.352 -0.031 1.00e-02 1.00e+04 9.37e+00 bond pdb=" CG HIS B 487 " pdb=" ND1 HIS B 487 " ideal model delta sigma weight residual 1.378 1.409 -0.031 1.10e-02 8.26e+03 7.95e+00 bond pdb=" ND1 HIS B 264 " pdb=" CE1 HIS B 264 " ideal model delta sigma weight residual 1.321 1.349 -0.028 1.00e-02 1.00e+04 7.71e+00 bond pdb=" N VAL A 97 " pdb=" CA VAL A 97 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.35e-02 5.49e+03 7.71e+00 ... (remaining 6096 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.05: 291 105.05 - 112.32: 3005 112.32 - 119.60: 2144 119.60 - 126.88: 2855 126.88 - 134.15: 175 Bond angle restraints: 8470 Sorted by residual: angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 102.13 10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" C ASP B 273 " ideal model delta sigma weight residual 113.12 102.64 10.48 1.25e+00 6.40e-01 7.04e+01 angle pdb=" N ALA B 187 " pdb=" CA ALA B 187 " pdb=" C ALA B 187 " ideal model delta sigma weight residual 111.07 118.72 -7.65 1.07e+00 8.73e-01 5.11e+01 angle pdb=" CB HIS B 487 " pdb=" CG HIS B 487 " pdb=" CD2 HIS B 487 " ideal model delta sigma weight residual 131.20 123.76 7.44 1.30e+00 5.92e-01 3.27e+01 angle pdb=" CA ALA B 187 " pdb=" C ALA B 187 " pdb=" O ALA B 187 " ideal model delta sigma weight residual 120.82 114.82 6.00 1.05e+00 9.07e-01 3.26e+01 ... (remaining 8465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.54: 3199 18.54 - 37.08: 278 37.08 - 55.61: 87 55.61 - 74.15: 44 74.15 - 92.69: 6 Dihedral angle restraints: 3614 sinusoidal: 1742 harmonic: 1872 Sorted by residual: dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TYR B 237 " pdb=" C TYR B 237 " pdb=" N ASN B 238 " pdb=" CA ASN B 238 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C PHE B 190 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " pdb=" CB PHE B 190 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 762 0.063 - 0.126: 158 0.126 - 0.190: 37 0.190 - 0.253: 5 0.253 - 0.316: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA LEU B 185 " pdb=" N LEU B 185 " pdb=" C LEU B 185 " pdb=" CB LEU B 185 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE B 231 " pdb=" CA ILE B 231 " pdb=" CG1 ILE B 231 " pdb=" CG2 ILE B 231 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA PHE B 190 " pdb=" N PHE B 190 " pdb=" C PHE B 190 " pdb=" CB PHE B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 961 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 83 " 0.100 2.00e-02 2.50e+03 7.39e-02 8.19e+01 pdb=" CG HIS A 83 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 83 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 HIS A 83 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 HIS A 83 " 0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 83 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 76 " -0.083 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR A 76 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 76 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 76 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 76 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 76 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 76 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 76 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 271 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C SER B 271 " -0.082 2.00e-02 2.50e+03 pdb=" O SER B 271 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS B 272 " 0.028 2.00e-02 2.50e+03 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 42 2.52 - 3.11: 4151 3.11 - 3.71: 9418 3.71 - 4.30: 12840 4.30 - 4.90: 20212 Nonbonded interactions: 46663 Sorted by model distance: nonbonded pdb="CA CA B 601 " pdb=" O HOH D 101 " model vdw 1.921 2.510 nonbonded pdb=" OP1 C D 71 " pdb="CA CA B 601 " model vdw 1.925 2.510 nonbonded pdb=" OD2 ASP B 90 " pdb="CA CA B 601 " model vdw 2.013 2.510 nonbonded pdb=" OD2 ASP B 273 " pdb="CA CA B 601 " model vdw 2.123 2.510 nonbonded pdb=" OD1 ASP B 90 " pdb="CA CA B 602 " model vdw 2.197 2.510 ... (remaining 46658 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6101 Z= 0.392 Angle : 1.104 10.826 8470 Z= 0.674 Chirality : 0.058 0.316 964 Planarity : 0.008 0.074 943 Dihedral : 16.966 92.688 2412 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.36 % Allowed : 7.58 % Favored : 92.06 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.27), residues: 637 helix: -3.30 (0.31), residues: 139 sheet: -2.38 (0.82), residues: 37 loop : -2.24 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 520 HIS 0.013 0.002 HIS B 229 PHE 0.023 0.003 PHE A 110 TYR 0.083 0.003 TYR A 76 ARG 0.005 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7419 (m-30) cc_final: 0.6871 (m-30) REVERT: A 98 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: B 92 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: B 195 MET cc_start: 0.8486 (mtt) cc_final: 0.8129 (mtt) REVERT: B 253 LEU cc_start: 0.7116 (tp) cc_final: 0.6790 (tp) REVERT: B 348 TRP cc_start: 0.6563 (t-100) cc_final: 0.6026 (t-100) REVERT: B 494 TYR cc_start: 0.8505 (t80) cc_final: 0.8234 (t80) REVERT: B 509 TRP cc_start: 0.8565 (m100) cc_final: 0.8321 (m100) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2204 time to fit residues: 38.9099 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 228 HIS B 229 HIS B 314 HIS B 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6101 Z= 0.186 Angle : 0.617 9.055 8470 Z= 0.315 Chirality : 0.041 0.179 964 Planarity : 0.005 0.052 943 Dihedral : 16.596 95.316 1270 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.71 % Allowed : 16.61 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.30), residues: 637 helix: -2.13 (0.36), residues: 151 sheet: -2.31 (0.58), residues: 64 loop : -1.51 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS B 330 PHE 0.016 0.002 PHE B 326 TYR 0.013 0.001 TYR B 447 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7831 (ttmm) REVERT: A 92 LEU cc_start: 0.8928 (mt) cc_final: 0.8712 (mt) REVERT: B 118 VAL cc_start: 0.8756 (t) cc_final: 0.8480 (m) REVERT: B 241 MET cc_start: 0.6949 (ptp) cc_final: 0.6679 (mtm) REVERT: B 253 LEU cc_start: 0.7213 (tp) cc_final: 0.7006 (tp) REVERT: B 254 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: B 447 TYR cc_start: 0.6892 (t80) cc_final: 0.6630 (t80) REVERT: B 509 TRP cc_start: 0.8508 (m100) cc_final: 0.8251 (m100) outliers start: 15 outliers final: 3 residues processed: 114 average time/residue: 0.1990 time to fit residues: 28.8073 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6101 Z= 0.420 Angle : 0.711 8.103 8470 Z= 0.372 Chirality : 0.044 0.159 964 Planarity : 0.005 0.052 943 Dihedral : 16.481 95.266 1264 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.79 % Allowed : 16.79 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.31), residues: 637 helix: -1.57 (0.39), residues: 145 sheet: -2.09 (0.52), residues: 70 loop : -1.48 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 348 HIS 0.017 0.002 HIS B 229 PHE 0.025 0.003 PHE B 133 TYR 0.019 0.002 TYR B 351 ARG 0.004 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TYR cc_start: 0.7530 (m-80) cc_final: 0.7214 (m-10) REVERT: B 72 MET cc_start: 0.8906 (mmm) cc_final: 0.8644 (mtp) REVERT: B 254 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: B 273 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7450 (t0) REVERT: B 348 TRP cc_start: 0.6905 (m-10) cc_final: 0.6359 (m-10) outliers start: 21 outliers final: 12 residues processed: 112 average time/residue: 0.1888 time to fit residues: 27.4664 Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 330 HIS B 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6101 Z= 0.230 Angle : 0.611 10.203 8470 Z= 0.312 Chirality : 0.041 0.189 964 Planarity : 0.004 0.045 943 Dihedral : 16.289 95.549 1264 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.61 % Allowed : 19.68 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.31), residues: 637 helix: -1.26 (0.41), residues: 146 sheet: -1.65 (0.60), residues: 60 loop : -1.38 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 509 HIS 0.017 0.001 HIS B 229 PHE 0.019 0.002 PHE B 133 TYR 0.012 0.001 TYR A 96 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 VAL cc_start: 0.9113 (m) cc_final: 0.8840 (p) REVERT: B 253 LEU cc_start: 0.7281 (tp) cc_final: 0.7060 (tt) REVERT: B 302 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 315 MET cc_start: 0.7679 (tmm) cc_final: 0.7330 (tmm) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.1791 time to fit residues: 25.0147 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 330 HIS B 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6101 Z= 0.216 Angle : 0.588 7.762 8470 Z= 0.301 Chirality : 0.040 0.145 964 Planarity : 0.004 0.045 943 Dihedral : 16.140 95.487 1264 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.07 % Allowed : 20.22 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.32), residues: 637 helix: -1.15 (0.41), residues: 147 sheet: -1.84 (0.54), residues: 66 loop : -1.13 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 348 HIS 0.017 0.001 HIS B 229 PHE 0.028 0.002 PHE B 436 TYR 0.016 0.001 TYR A 27 ARG 0.004 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8920 (t) cc_final: 0.8614 (p) REVERT: A 119 VAL cc_start: 0.9115 (m) cc_final: 0.8835 (p) REVERT: B 195 MET cc_start: 0.8194 (ttm) cc_final: 0.7889 (ttm) REVERT: B 241 MET cc_start: 0.6841 (ptp) cc_final: 0.6530 (mtm) REVERT: B 253 LEU cc_start: 0.7470 (tp) cc_final: 0.7234 (tt) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.1735 time to fit residues: 22.8248 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6101 Z= 0.194 Angle : 0.570 8.191 8470 Z= 0.290 Chirality : 0.040 0.134 964 Planarity : 0.004 0.045 943 Dihedral : 15.994 95.286 1264 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.61 % Allowed : 20.76 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 637 helix: -0.97 (0.41), residues: 149 sheet: -1.61 (0.56), residues: 64 loop : -1.04 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 509 HIS 0.017 0.001 HIS B 229 PHE 0.024 0.002 PHE B 436 TYR 0.027 0.001 TYR B 447 ARG 0.002 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8849 (t) cc_final: 0.8570 (p) REVERT: A 119 VAL cc_start: 0.9107 (m) cc_final: 0.8825 (p) REVERT: B 195 MET cc_start: 0.8116 (ttm) cc_final: 0.7769 (ttm) REVERT: B 241 MET cc_start: 0.6791 (ptp) cc_final: 0.6446 (mtm) REVERT: B 253 LEU cc_start: 0.7540 (tp) cc_final: 0.7218 (tt) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.1804 time to fit residues: 25.7586 Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8822 > 50: distance: 45 - 58: 3.048 distance: 50 - 71: 25.972 distance: 57 - 78: 24.938 distance: 60 - 66: 28.163 distance: 61 - 88: 14.442 distance: 66 - 67: 17.747 distance: 67 - 68: 13.119 distance: 67 - 70: 3.864 distance: 68 - 69: 26.520 distance: 68 - 71: 5.913 distance: 71 - 72: 15.988 distance: 72 - 73: 18.702 distance: 72 - 75: 7.380 distance: 73 - 74: 10.352 distance: 73 - 78: 6.992 distance: 74 - 103: 21.472 distance: 75 - 76: 12.770 distance: 75 - 77: 35.522 distance: 78 - 79: 13.470 distance: 79 - 80: 6.722 distance: 79 - 82: 4.351 distance: 80 - 81: 15.079 distance: 80 - 88: 9.324 distance: 81 - 114: 18.247 distance: 82 - 83: 6.904 distance: 83 - 84: 10.929 distance: 83 - 85: 22.391 distance: 84 - 86: 14.419 distance: 85 - 87: 14.260 distance: 86 - 87: 19.101 distance: 88 - 89: 13.620 distance: 89 - 90: 10.230 distance: 89 - 92: 19.347 distance: 90 - 91: 41.848 distance: 90 - 97: 16.901 distance: 92 - 93: 12.463 distance: 93 - 94: 5.164 distance: 94 - 95: 26.771 distance: 94 - 96: 7.114 distance: 97 - 98: 15.709 distance: 98 - 99: 11.725 distance: 98 - 101: 17.951 distance: 99 - 100: 24.701 distance: 99 - 103: 18.331 distance: 101 - 102: 49.023 distance: 103 - 104: 10.053 distance: 104 - 105: 13.180 distance: 104 - 107: 16.756 distance: 105 - 106: 18.539 distance: 105 - 114: 17.379 distance: 107 - 108: 12.155 distance: 108 - 109: 11.828 distance: 108 - 110: 20.548 distance: 109 - 111: 10.864 distance: 110 - 112: 23.304 distance: 111 - 113: 10.161 distance: 112 - 113: 19.020 distance: 114 - 115: 7.146 distance: 115 - 116: 22.870 distance: 115 - 118: 32.699 distance: 116 - 117: 9.248 distance: 116 - 121: 22.895 distance: 118 - 119: 11.057 distance: 118 - 120: 27.198 distance: 121 - 122: 13.601 distance: 122 - 123: 10.519 distance: 122 - 125: 18.784 distance: 123 - 124: 5.669 distance: 123 - 130: 17.548 distance: 125 - 126: 10.110 distance: 126 - 127: 28.083 distance: 127 - 128: 16.468 distance: 128 - 129: 4.170 distance: 130 - 131: 30.292 distance: 131 - 132: 20.919 distance: 131 - 134: 12.156 distance: 132 - 133: 15.868 distance: 132 - 141: 11.825 distance: 134 - 135: 22.704 distance: 135 - 136: 13.827 distance: 136 - 137: 12.221 distance: 137 - 138: 12.220 distance: 138 - 139: 30.630 distance: 138 - 140: 16.972 distance: 141 - 142: 28.853 distance: 142 - 143: 18.473 distance: 142 - 145: 38.965 distance: 143 - 144: 17.083 distance: 143 - 148: 20.195 distance: 145 - 146: 12.607 distance: 145 - 147: 10.836