Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:37:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhp_29098/04_2023/8fhp_29098_updated.pdb" } resolution = 3.04 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= -0.001 sd= 0.051 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 S 48 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4836 2.51 5 N 1144 2.21 5 O 1268 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3627 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.17, per 1000 atoms: 0.57 Number of scatterers: 7306 At special positions: 0 Unit cell: (92.02, 107.5, 94.6, 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) Cl 2 17.00 S 48 16.00 Na 2 11.00 F 6 9.00 O 1268 8.00 N 1144 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " 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: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.628A pdb=" N ALA A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 195 removed outlier: 3.753A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 213 through 249 removed outlier: 3.886A pdb=" N GLY A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 Processing helix chain 'A' and resid 280 through 305 removed outlier: 4.116A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 340 through 350 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 367 through 395 Proline residue: A 372 - end of helix removed outlier: 3.660A pdb=" N SER A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 419 through 422 removed outlier: 3.825A pdb=" N SER A 422 " --> pdb=" O LEU A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 447 through 450 No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 454 through 483 removed outlier: 3.649A pdb=" N THR A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.570A pdb=" N GLY A 493 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 495 " --> pdb=" O ILE A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 490 through 495' Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.549A pdb=" N LEU A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.629A pdb=" N LEU A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.881A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.628A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 195 removed outlier: 3.753A pdb=" N THR B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 213 through 249 removed outlier: 3.887A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 276 Processing helix chain 'B' and resid 280 through 305 removed outlier: 4.116A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 340 through 350 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 367 through 395 Proline residue: B 372 - end of helix removed outlier: 3.659A pdb=" N SER B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 419 through 422 removed outlier: 3.824A pdb=" N SER B 422 " --> pdb=" O LEU B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 454 through 483 removed outlier: 3.649A pdb=" N THR B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.570A pdb=" N GLY B 493 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 495 " --> pdb=" O ILE B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 506 through 522 removed outlier: 3.549A pdb=" N LEU B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 552 removed outlier: 3.628A pdb=" N LEU B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 544 " --> pdb=" O TYR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.881A pdb=" N VAL B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 378 hydrogen bonds defined for protein. 1134 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: 1.80 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1100 1.31 - 1.44: 2154 1.44 - 1.56: 4174 1.56 - 1.68: 4 1.68 - 1.81: 72 Bond restraints: 7504 Sorted by residual: bond pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.37e-02 5.33e+03 1.40e+01 bond pdb=" C ASN A 149 " pdb=" O ASN A 149 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.29e-02 6.01e+03 1.37e+01 bond pdb=" C ASN B 149 " pdb=" O ASN B 149 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.32e-02 5.74e+03 8.64e+00 bond pdb=" C16 XZF B1101 " pdb=" C17 XZF B1101 " ideal model delta sigma weight residual 1.368 1.315 0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C16 XZF A1101 " pdb=" C17 XZF A1101 " ideal model delta sigma weight residual 1.368 1.315 0.053 2.00e-02 2.50e+03 7.03e+00 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 170 106.24 - 113.19: 4090 113.19 - 120.14: 2893 120.14 - 127.09: 3010 127.09 - 134.03: 93 Bond angle restraints: 10256 Sorted by residual: angle pdb=" O LEU B 148 " pdb=" C LEU B 148 " pdb=" N ASN B 149 " ideal model delta sigma weight residual 122.27 115.44 6.83 1.23e+00 6.61e-01 3.08e+01 angle pdb=" CA LEU B 148 " pdb=" C LEU B 148 " pdb=" N ASN B 149 " ideal model delta sigma weight residual 117.72 124.75 -7.03 1.31e+00 5.83e-01 2.88e+01 angle pdb=" N ILE A 369 " pdb=" CA ILE A 369 " pdb=" C ILE A 369 " ideal model delta sigma weight residual 113.53 108.64 4.89 9.80e-01 1.04e+00 2.48e+01 angle pdb=" N ILE B 369 " pdb=" CA ILE B 369 " pdb=" C ILE B 369 " ideal model delta sigma weight residual 113.53 108.65 4.88 9.80e-01 1.04e+00 2.48e+01 angle pdb=" C ASN B 149 " pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 120.74 115.10 5.64 1.43e+00 4.89e-01 1.55e+01 ... (remaining 10251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3907 17.88 - 35.77: 289 35.77 - 53.65: 52 53.65 - 71.53: 14 71.53 - 89.42: 2 Dihedral angle restraints: 4264 sinusoidal: 1554 harmonic: 2710 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 153.00 -60.00 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA GLU B 214 " pdb=" C GLU B 214 " pdb=" N LEU B 215 " pdb=" CA LEU B 215 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 485 0.029 - 0.058: 418 0.058 - 0.087: 212 0.087 - 0.116: 66 0.116 - 0.145: 11 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA ASN A 149 " pdb=" N ASN A 149 " pdb=" C ASN A 149 " pdb=" CB ASN A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" C PRO B 367 " pdb=" CB PRO B 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1189 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 489 " 0.051 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO A 490 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 489 " -0.051 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 490 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 212 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 213 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.025 5.00e-02 4.00e+02 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1483 2.76 - 3.30: 6989 3.30 - 3.83: 11715 3.83 - 4.37: 13722 4.37 - 4.90: 24445 Nonbonded interactions: 58354 Sorted by model distance: nonbonded pdb=" O ALA A 164 " pdb=" NH1 ARG A 399 " model vdw 2.227 2.520 nonbonded pdb=" O ALA B 164 " pdb=" NH1 ARG B 399 " model vdw 2.228 2.520 nonbonded pdb=" OH TYR B 156 " pdb=" OG SER B 296 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR A 156 " pdb=" OG SER A 296 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 468 " pdb="NA NA A1102 " model vdw 2.266 2.470 ... (remaining 58349 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' } 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 individual isotropic 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: 1.400 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: 7.420 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.190 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.057 7504 Z= 0.595 Angle : 0.797 7.032 10256 Z= 0.438 Chirality : 0.048 0.145 1192 Planarity : 0.006 0.079 1246 Dihedral : 13.082 89.418 2528 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.39 % 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: -1.88 (0.26), residues: 946 helix: -0.48 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.75 (0.28), residues: 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.941 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 107 average time/residue: 0.2155 time to fit residues: 30.9185 Evaluate side-chains 90 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 234 HIS B 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7504 Z= 0.179 Angle : 0.517 10.698 10256 Z= 0.258 Chirality : 0.039 0.134 1192 Planarity : 0.005 0.041 1246 Dihedral : 4.740 29.981 1020 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 946 helix: 0.44 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.787 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.1956 time to fit residues: 26.3225 Evaluate side-chains 87 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1520 time to fit residues: 2.1907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 7504 Z= 0.358 Angle : 0.591 10.534 10256 Z= 0.292 Chirality : 0.042 0.139 1192 Planarity : 0.005 0.036 1246 Dihedral : 4.911 34.017 1020 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 946 helix: 0.38 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.808 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 95 average time/residue: 0.2048 time to fit residues: 26.5526 Evaluate side-chains 93 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0686 time to fit residues: 2.1395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7504 Z= 0.189 Angle : 0.496 10.451 10256 Z= 0.242 Chirality : 0.039 0.137 1192 Planarity : 0.004 0.039 1246 Dihedral : 4.477 32.559 1020 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 946 helix: 0.81 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.54 (0.29), residues: 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.788 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.1972 time to fit residues: 27.8657 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0842 time to fit residues: 1.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 7504 Z= 0.152 Angle : 0.463 9.664 10256 Z= 0.224 Chirality : 0.038 0.145 1192 Planarity : 0.004 0.038 1246 Dihedral : 4.153 31.625 1020 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 946 helix: 1.10 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.38 (0.30), residues: 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.779 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2029 time to fit residues: 27.1494 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0766 time to fit residues: 1.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 7504 Z= 0.147 Angle : 0.449 8.323 10256 Z= 0.219 Chirality : 0.038 0.148 1192 Planarity : 0.004 0.037 1246 Dihedral : 4.016 31.120 1020 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 946 helix: 1.35 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.935 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.2175 time to fit residues: 28.8238 Evaluate side-chains 96 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1798 time to fit residues: 2.3492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7504 Z= 0.164 Angle : 0.456 7.884 10256 Z= 0.223 Chirality : 0.038 0.142 1192 Planarity : 0.004 0.036 1246 Dihedral : 4.005 31.319 1020 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 946 helix: 1.41 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.22 (0.30), residues: 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.827 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.2027 time to fit residues: 25.9397 Evaluate side-chains 95 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0688 time to fit residues: 1.3755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 86 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7504 Z= 0.132 Angle : 0.440 7.654 10256 Z= 0.216 Chirality : 0.038 0.152 1192 Planarity : 0.004 0.048 1246 Dihedral : 3.847 29.549 1020 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 946 helix: 1.58 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.705 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.2001 time to fit residues: 25.9599 Evaluate side-chains 86 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 7504 Z= 0.294 Angle : 0.528 7.736 10256 Z= 0.262 Chirality : 0.041 0.156 1192 Planarity : 0.004 0.042 1246 Dihedral : 4.248 31.648 1020 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 946 helix: 1.25 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.722 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.2107 time to fit residues: 27.9882 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0729 time to fit residues: 1.3781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.0020 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7504 Z= 0.160 Angle : 0.458 7.983 10256 Z= 0.227 Chirality : 0.038 0.146 1192 Planarity : 0.004 0.045 1246 Dihedral : 4.026 29.771 1020 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 946 helix: 1.45 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.10 (0.30), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2042 time to fit residues: 25.4278 Evaluate side-chains 87 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111078 restraints weight = 7739.528| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.40 r_work: 0.3043 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7504 Z= 0.159 Angle : 0.465 8.246 10256 Z= 0.228 Chirality : 0.038 0.160 1192 Planarity : 0.004 0.041 1246 Dihedral : 3.947 27.360 1020 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 946 helix: 1.58 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 306 =============================================================================== Job complete usr+sys time: 1746.41 seconds wall clock time: 32 minutes 25.00 seconds (1945.00 seconds total)