Starting phenix.real_space_refine (version: dev) on Sun Feb 19 13:00:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f07_4163/02_2023/6f07_4163.pdb" } resolution = 3.6 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= 0.010 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 "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 336": "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: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4249 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 16, 'TRANS': 493} Chain breaks: 2 Chain: "B" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4746 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 132} Chain breaks: 2 Chain: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4346 SG CYS B 14 22.504 74.855 65.425 1.00228.19 S ATOM 4425 SG CYS B 24 25.564 72.810 64.715 1.00223.95 S ATOM 4346 SG CYS B 14 22.504 74.855 65.425 1.00228.19 S ATOM 4473 SG CYS B 30 25.268 77.024 64.816 1.00203.85 S ATOM 4491 SG CYS B 33 22.225 78.973 63.646 1.00205.77 S ATOM 4564 SG CYS B 42 22.697 77.660 67.746 1.00216.67 S Time building chain proxies: 5.94, per 1000 atoms: 0.59 Number of scatterers: 10149 At special positions: 0 Unit cell: (119.658, 112.112, 120.736, 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) Zn 2 29.99 S 54 16.00 O 1872 8.00 N 1670 7.00 C 6551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 24 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 30 " Number of angles added : 6 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 73.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.613A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.877A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 removed outlier: 4.095A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 243 No H-bonds generated for 'chain 'A' and resid 242 through 243' Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.542A pdb=" N ASP A 248 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.529A pdb=" N SER A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 393 through 422 Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 456 through 477 removed outlier: 4.079A pdb=" N MET A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.819A pdb=" N ALA A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 496 No H-bonds generated for 'chain 'A' and resid 495 through 496' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 523 removed outlier: 3.640A pdb=" N LEU A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 3.758A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.859A pdb=" N GLY A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.524A pdb=" N LEU A 607 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.509A pdb=" N ARG B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.732A pdb=" N CYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.682A pdb=" N LEU B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.813A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.887A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.055A pdb=" N LEU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 173 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.723A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.531A pdb=" N VAL B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.696A pdb=" N HIS B 228 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.437A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.015A pdb=" N GLU B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 341 through 357 removed outlier: 3.791A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.751A pdb=" N LEU B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 Processing helix chain 'B' and resid 426 through 444 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.973A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 494 Processing helix chain 'B' and resid 495 through 496 No H-bonds generated for 'chain 'B' and resid 495 through 496' Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 523 removed outlier: 3.546A pdb=" N LEU B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.663A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 3.948A pdb=" N GLY B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 602 through 606 removed outlier: 3.937A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.608A pdb=" N ALA D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.126A pdb=" N TYR A 534 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 18 removed outlier: 6.459A pdb=" N VAL D 7 " --> pdb=" O MET D 77 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3061 1.34 - 1.46: 2009 1.46 - 1.58: 5223 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10378 Sorted by residual: bond pdb=" CA ASN B 543 " pdb=" C ASN B 543 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.20e-02 6.94e+03 2.77e+00 bond pdb=" C SER B 363 " pdb=" N LYS B 364 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.36e-02 5.41e+03 2.32e+00 bond pdb=" N ASN B 543 " pdb=" CA ASN B 543 " ideal model delta sigma weight residual 1.460 1.443 0.017 1.14e-02 7.69e+03 2.29e+00 bond pdb=" C LEU A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.20e+00 bond pdb=" CA LEU A 58 " pdb=" C LEU A 58 " ideal model delta sigma weight residual 1.521 1.538 -0.017 1.14e-02 7.69e+03 2.18e+00 ... (remaining 10373 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.06: 189 106.06 - 113.06: 5555 113.06 - 120.06: 3978 120.06 - 127.06: 4211 127.06 - 134.06: 105 Bond angle restraints: 14038 Sorted by residual: angle pdb=" N ASN B 543 " pdb=" CA ASN B 543 " pdb=" C ASN B 543 " ideal model delta sigma weight residual 114.62 100.96 13.66 1.14e+00 7.69e-01 1.43e+02 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 113.53 107.58 5.95 9.80e-01 1.04e+00 3.68e+01 angle pdb=" N THR B 6 " pdb=" CA THR B 6 " pdb=" C THR B 6 " ideal model delta sigma weight residual 108.76 116.77 -8.01 1.58e+00 4.01e-01 2.57e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 114.56 108.84 5.72 1.27e+00 6.20e-01 2.03e+01 angle pdb=" C VAL B 185 " pdb=" N TYR B 186 " pdb=" CA TYR B 186 " ideal model delta sigma weight residual 120.09 125.49 -5.40 1.25e+00 6.40e-01 1.87e+01 ... (remaining 14033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5875 15.42 - 30.84: 300 30.84 - 46.27: 62 46.27 - 61.69: 7 61.69 - 77.11: 8 Dihedral angle restraints: 6252 sinusoidal: 2588 harmonic: 3664 Sorted by residual: dihedral pdb=" CA LEU B 312 " pdb=" C LEU B 312 " pdb=" N HIS B 313 " pdb=" CA HIS B 313 " ideal model delta harmonic sigma weight residual 180.00 142.37 37.63 0 5.00e+00 4.00e-02 5.66e+01 dihedral pdb=" CA LEU B 8 " pdb=" C LEU B 8 " pdb=" N LYS B 9 " pdb=" CA LYS B 9 " ideal model delta harmonic sigma weight residual -180.00 -149.13 -30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA MET B 27 " pdb=" C MET B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 993 0.046 - 0.092: 431 0.092 - 0.138: 115 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 1556 Sorted by residual: chirality pdb=" CA ASN B 543 " pdb=" N ASN B 543 " pdb=" C ASN B 543 " pdb=" CB ASN B 543 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 28 " pdb=" CA ILE B 28 " pdb=" CG1 ILE B 28 " pdb=" CG2 ILE B 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1553 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 245 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO A 246 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 245 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO B 246 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 508 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL B 508 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL B 508 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 509 " -0.015 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 8 1.43 - 2.30: 28 2.30 - 3.16: 8494 3.16 - 4.03: 24622 4.03 - 4.90: 44139 Warning: very small nonbonded interaction distances. Nonbonded interactions: 77291 Sorted by model distance: nonbonded pdb=" NE2 HIS B 12 " pdb=" N PHE D 176 " model vdw 0.559 3.200 nonbonded pdb=" CB HIS B 12 " pdb=" CG PHE D 176 " model vdw 0.707 3.660 nonbonded pdb=" CG HIS B 12 " pdb=" CG PHE D 176 " model vdw 0.866 3.480 nonbonded pdb=" CB HIS B 12 " pdb=" CD2 PHE D 176 " model vdw 1.161 3.740 nonbonded pdb=" CG HIS B 12 " pdb=" CD1 PHE D 176 " model vdw 1.165 3.560 ... (remaining 77286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 55 through 313 or resid 336 through 565 or resid 588 throu \ gh 608)) } 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 Zn 2 6.06 5 S 54 5.16 5 C 6551 2.51 5 N 1670 2.21 5 O 1872 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=0.00 max=1.00 mean=0.99 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: 0.500 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: 3.840 Check model and map are aligned: 0.170 Process input model: 29.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 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 : 0.007 0.068 10378 Z= 0.422 Angle : 0.958 13.656 14038 Z= 0.565 Chirality : 0.053 0.230 1556 Planarity : 0.008 0.079 1769 Dihedral : 10.285 77.111 3863 Min Nonbonded Distance : 0.559 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.71 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.04 (0.19), residues: 1209 helix: -1.48 (0.14), residues: 817 sheet: 0.48 (1.77), residues: 14 loop : -3.08 (0.26), residues: 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 300 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 306 average time/residue: 0.2861 time to fit residues: 114.9992 Evaluate side-chains 150 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0924 time to fit residues: 1.8962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 142 GLN A 394 ASN A 461 GLN A 474 GLN A 543 ASN B 12 HIS B 66 GLN B 67 ASN B 228 HIS B 303 GLN B 399 GLN B 406 GLN B 445 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10378 Z= 0.185 Angle : 0.596 9.021 14038 Z= 0.317 Chirality : 0.039 0.199 1556 Planarity : 0.005 0.071 1769 Dihedral : 5.022 30.361 1340 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.61 (0.23), residues: 1209 helix: 0.47 (0.17), residues: 835 sheet: 0.24 (1.73), residues: 14 loop : -2.49 (0.30), residues: 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 198 average time/residue: 0.2346 time to fit residues: 64.9890 Evaluate side-chains 135 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1092 time to fit residues: 4.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10378 Z= 0.165 Angle : 0.548 7.749 14038 Z= 0.288 Chirality : 0.038 0.118 1556 Planarity : 0.005 0.056 1769 Dihedral : 4.514 27.847 1340 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1209 helix: 1.13 (0.18), residues: 850 sheet: -0.30 (1.63), residues: 14 loop : -2.31 (0.30), residues: 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 166 average time/residue: 0.2390 time to fit residues: 55.4833 Evaluate side-chains 130 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1001 time to fit residues: 2.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10378 Z= 0.268 Angle : 0.645 8.360 14038 Z= 0.338 Chirality : 0.042 0.160 1556 Planarity : 0.005 0.048 1769 Dihedral : 4.748 25.502 1340 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.20 (0.24), residues: 1209 helix: 1.10 (0.18), residues: 849 sheet: -0.37 (1.66), residues: 14 loop : -2.34 (0.30), residues: 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 167 average time/residue: 0.2295 time to fit residues: 53.9127 Evaluate side-chains 134 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1065 time to fit residues: 3.9738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 433 HIS D 34 ASN D 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10378 Z= 0.212 Angle : 0.588 7.348 14038 Z= 0.306 Chirality : 0.040 0.136 1556 Planarity : 0.004 0.044 1769 Dihedral : 4.572 25.399 1340 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1209 helix: 1.26 (0.18), residues: 853 sheet: -0.53 (1.58), residues: 14 loop : -2.23 (0.31), residues: 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 157 average time/residue: 0.2347 time to fit residues: 52.4037 Evaluate side-chains 144 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1176 time to fit residues: 4.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10378 Z= 0.205 Angle : 0.577 8.853 14038 Z= 0.301 Chirality : 0.039 0.130 1556 Planarity : 0.004 0.044 1769 Dihedral : 4.463 23.870 1340 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.63 (0.25), residues: 1209 helix: 1.40 (0.18), residues: 851 sheet: -0.61 (1.54), residues: 14 loop : -2.09 (0.32), residues: 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 155 average time/residue: 0.2232 time to fit residues: 50.1389 Evaluate side-chains 136 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0990 time to fit residues: 2.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10378 Z= 0.227 Angle : 0.602 8.494 14038 Z= 0.313 Chirality : 0.040 0.145 1556 Planarity : 0.004 0.042 1769 Dihedral : 4.530 24.694 1340 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.58 (0.25), residues: 1209 helix: 1.37 (0.18), residues: 850 sheet: -0.74 (1.48), residues: 14 loop : -2.12 (0.31), residues: 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 141 average time/residue: 0.2197 time to fit residues: 45.1285 Evaluate side-chains 130 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0954 time to fit residues: 2.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10378 Z= 0.191 Angle : 0.585 9.270 14038 Z= 0.301 Chirality : 0.039 0.166 1556 Planarity : 0.004 0.043 1769 Dihedral : 4.368 24.640 1340 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1209 helix: 1.50 (0.18), residues: 845 sheet: -0.64 (1.45), residues: 14 loop : -2.02 (0.31), residues: 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 144 average time/residue: 0.2249 time to fit residues: 47.2761 Evaluate side-chains 131 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0949 time to fit residues: 2.8700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10378 Z= 0.214 Angle : 0.609 10.454 14038 Z= 0.315 Chirality : 0.040 0.196 1556 Planarity : 0.004 0.040 1769 Dihedral : 4.402 24.945 1340 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.69 (0.25), residues: 1209 helix: 1.46 (0.18), residues: 845 sheet: -0.77 (1.34), residues: 14 loop : -2.05 (0.31), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.2203 time to fit residues: 41.6189 Evaluate side-chains 124 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1396 time to fit residues: 1.9758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10378 Z= 0.163 Angle : 0.573 9.733 14038 Z= 0.295 Chirality : 0.039 0.218 1556 Planarity : 0.004 0.042 1769 Dihedral : 4.209 25.296 1340 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.90 (0.25), residues: 1209 helix: 1.58 (0.18), residues: 846 sheet: -0.32 (1.33), residues: 14 loop : -1.89 (0.32), residues: 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2123 time to fit residues: 45.5944 Evaluate side-chains 132 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0961 time to fit residues: 1.8733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.175071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156841 restraints weight = 17148.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.159395 restraints weight = 10892.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161056 restraints weight = 8009.342| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10378 Z= 0.177 Angle : 0.584 8.540 14038 Z= 0.299 Chirality : 0.039 0.199 1556 Planarity : 0.004 0.043 1769 Dihedral : 4.206 24.729 1340 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % 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: 0.95 (0.25), residues: 1209 helix: 1.61 (0.18), residues: 852 sheet: -0.14 (1.48), residues: 14 loop : -1.91 (0.32), residues: 343 =============================================================================== Job complete usr+sys time: 1921.02 seconds wall clock time: 36 minutes 12.59 seconds (2172.59 seconds total)