Starting phenix.real_space_refine (version: dev) on Wed Apr 6 05:02:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2p_23136/04_2022/7l2p_23136_updated.pdb" } resolution = 2.6 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 142": "NH1" <-> "NH2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 18448 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 15, 'TRANS': 602, 'PCIS': 1} Chain: "D" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4363 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 13, 'TRANS': 522, 'PCIS': 1} Chain: "B" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4432 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 13, 'TRANS': 531, 'PCIS': 1} Chain: "C" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4324 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 517, 'PCIS': 1} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {' NA': 1, 'XJ7': 1, '6IY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'XJ7': 1, '6IY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'XJ7': 1, '6IY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.10, per 1000 atoms: 0.55 Number of scatterers: 18448 At special positions: 0 Unit cell: (123.903, 131.316, 119.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 8 15.00 Na 1 11.00 O 3315 8.00 N 2947 7.00 C 12074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " 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: 7.47 Conformation dependent library (CDL) restraints added in 2.8 seconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 4 sheets defined 57.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.544A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.100A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.563A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 4.066A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 removed outlier: 4.179A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 686 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 removed outlier: 3.502A pdb=" N TYR D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.773A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.568A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.153A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.933A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.804A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.535A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.943A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.994A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 497 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.563A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.900A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.964A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 710 removed outlier: 3.849A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.186A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 4.070A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.745A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.806A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2487 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: 4.99 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2847 1.31 - 1.43: 5333 1.43 - 1.56: 10482 1.56 - 1.69: 44 1.69 - 1.81: 168 Bond restraints: 18874 Sorted by residual: bond pdb=" C GLU A 249 " pdb=" N LEU A 250 " ideal model delta sigma weight residual 1.327 1.394 -0.067 1.71e-02 3.42e+03 1.55e+01 bond pdb=" O5 XJ7 A 801 " pdb=" P XJ7 A 801 " ideal model delta sigma weight residual 1.514 1.452 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O5 XJ7 C 801 " pdb=" P XJ7 C 801 " ideal model delta sigma weight residual 1.514 1.452 0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" O4 XJ7 D 801 " pdb=" P XJ7 D 801 " ideal model delta sigma weight residual 1.511 1.450 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" O4 XJ7 A 801 " pdb=" P XJ7 A 801 " ideal model delta sigma weight residual 1.511 1.451 0.060 2.00e-02 2.50e+03 9.09e+00 ... (remaining 18869 not shown) Histogram of bond angle deviations from ideal: 97.11 - 105.21: 242 105.21 - 113.31: 10165 113.31 - 121.41: 11084 121.41 - 129.51: 3882 129.51 - 137.61: 141 Bond angle restraints: 25514 Sorted by residual: angle pdb=" O4 XJ7 B 801 " pdb=" P XJ7 B 801 " pdb=" O5 XJ7 B 801 " ideal model delta sigma weight residual 142.14 100.35 41.79 3.00e+00 1.11e-01 1.94e+02 angle pdb=" O4 XJ7 D 801 " pdb=" P XJ7 D 801 " pdb=" O5 XJ7 D 801 " ideal model delta sigma weight residual 142.14 100.51 41.63 3.00e+00 1.11e-01 1.93e+02 angle pdb=" O4 XJ7 A 801 " pdb=" P XJ7 A 801 " pdb=" O5 XJ7 A 801 " ideal model delta sigma weight residual 142.14 100.55 41.59 3.00e+00 1.11e-01 1.92e+02 angle pdb=" O4 XJ7 C 801 " pdb=" P XJ7 C 801 " pdb=" O5 XJ7 C 801 " ideal model delta sigma weight residual 142.14 100.98 41.16 3.00e+00 1.11e-01 1.88e+02 angle pdb=" O3 XJ7 A 801 " pdb=" P XJ7 A 801 " pdb=" O6 XJ7 A 801 " ideal model delta sigma weight residual 142.27 110.66 31.61 3.00e+00 1.11e-01 1.11e+02 ... (remaining 25509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 10924 34.45 - 68.89: 147 68.89 - 103.34: 18 103.34 - 137.79: 2 137.79 - 172.23: 6 Dihedral angle restraints: 11097 sinusoidal: 4513 harmonic: 6584 Sorted by residual: dihedral pdb=" CA ARG C 721 " pdb=" C ARG C 721 " pdb=" N SER C 722 " pdb=" CA SER C 722 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 11094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.010: 2854 1.010 - 2.020: 0 2.020 - 3.030: 0 3.030 - 4.040: 0 4.040 - 5.051: 8 Chirality restraints: 2862 Sorted by residual: chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.53 -5.05 2.00e-01 2.50e+01 6.38e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.05 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.36e+02 ... (remaining 2859 not shown) Planarity restraints: 3139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ALA A 719 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE A 720 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 426 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C TRP B 426 " -0.035 2.00e-02 2.50e+03 pdb=" O TRP B 426 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B 427 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 727 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C GLN B 727 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 727 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL B 728 " -0.012 2.00e-02 2.50e+03 ... (remaining 3136 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 190 2.64 - 3.21: 17415 3.21 - 3.77: 28620 3.77 - 4.34: 40711 4.34 - 4.90: 66833 Nonbonded interactions: 153769 Sorted by model distance: nonbonded pdb=" OE2 GLU A 570 " pdb=" O11 XJ7 A 801 " model vdw 2.080 2.440 nonbonded pdb=" O GLY A 643 " pdb="NA NA A 804 " model vdw 2.119 2.470 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.153 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.160 2.440 nonbonded pdb=" OE2 GLU B 570 " pdb=" O11 XJ7 B 801 " model vdw 2.172 2.440 ... (remaining 153764 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' and resid 198 through 752) selection = (chain 'B' and resid 198 through 752) selection = (chain 'C' and resid 198 through 752) selection = (chain 'D' and resid 198 through 752) } 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 103 5.16 5 Na 1 4.78 5 C 12074 2.51 5 N 2947 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.870 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: 0.020 Extract box with map and model: 5.530 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 47.240 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 18874 Z= 0.396 Angle : 1.288 41.794 25514 Z= 0.552 Chirality : 0.269 5.051 2862 Planarity : 0.004 0.045 3139 Dihedral : 13.149 172.234 6864 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.35 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.13 (0.18), residues: 2226 helix: 1.08 (0.13), residues: 1382 sheet: -1.46 (0.55), residues: 71 loop : -1.58 (0.22), residues: 773 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 570 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 576 average time/residue: 1.2651 time to fit residues: 813.3374 Evaluate side-chains 346 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 342 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.3223 time to fit residues: 4.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN B 202 GLN B 228 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 691 GLN C 260 GLN C 410 HIS C 419 ASN C 687 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 18874 Z= 0.206 Angle : 0.657 16.451 25514 Z= 0.313 Chirality : 0.045 0.627 2862 Planarity : 0.005 0.094 3139 Dihedral : 12.326 176.442 2607 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.93 % Favored : 93.94 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.64 (0.18), residues: 2226 helix: 1.57 (0.14), residues: 1377 sheet: -1.34 (0.56), residues: 76 loop : -1.54 (0.23), residues: 773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 361 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 18 residues processed: 382 average time/residue: 1.1682 time to fit residues: 509.0130 Evaluate side-chains 353 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 335 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.2706 time to fit residues: 6.4405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 560 GLN A 727 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN D 560 GLN D 561 GLN B 260 GLN B 561 GLN C 393 ASN C 687 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.104 18874 Z= 0.455 Angle : 0.735 15.263 25514 Z= 0.362 Chirality : 0.048 0.499 2862 Planarity : 0.006 0.085 3139 Dihedral : 12.434 176.975 2607 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.20 % Favored : 93.44 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.29 (0.18), residues: 2226 helix: 1.22 (0.13), residues: 1353 sheet: -1.12 (0.59), residues: 76 loop : -1.46 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 311 time to evaluate : 2.416 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 34 residues processed: 352 average time/residue: 1.2059 time to fit residues: 479.4396 Evaluate side-chains 324 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 16 residues processed: 18 average time/residue: 0.4455 time to fit residues: 13.6786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 22 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 191 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 393 ASN C 687 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.081 18874 Z= 0.150 Angle : 0.628 15.469 25514 Z= 0.298 Chirality : 0.039 0.361 2862 Planarity : 0.004 0.069 3139 Dihedral : 11.897 178.462 2607 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.03 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.78 (0.18), residues: 2226 helix: 1.69 (0.14), residues: 1361 sheet: -0.72 (0.59), residues: 76 loop : -1.50 (0.22), residues: 789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 334 time to evaluate : 2.363 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 360 average time/residue: 1.1902 time to fit residues: 487.4808 Evaluate side-chains 335 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.2296 time to fit residues: 7.6635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 159 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 560 GLN C 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 18874 Z= 0.240 Angle : 0.641 15.378 25514 Z= 0.308 Chirality : 0.041 0.376 2862 Planarity : 0.005 0.077 3139 Dihedral : 11.765 179.538 2607 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.35 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2226 helix: 1.68 (0.14), residues: 1357 sheet: -0.62 (0.59), residues: 76 loop : -1.44 (0.22), residues: 793 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 305 time to evaluate : 2.182 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 34 residues processed: 340 average time/residue: 1.2081 time to fit residues: 466.1250 Evaluate side-chains 325 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 291 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 17 residues processed: 17 average time/residue: 0.3744 time to fit residues: 11.9228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 393 ASN C 687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 18874 Z= 0.154 Angle : 0.629 15.602 25514 Z= 0.296 Chirality : 0.039 0.351 2862 Planarity : 0.004 0.075 3139 Dihedral : 11.405 176.650 2607 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.62 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.93 (0.18), residues: 2226 helix: 1.82 (0.14), residues: 1361 sheet: -0.54 (0.58), residues: 76 loop : -1.48 (0.22), residues: 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 310 time to evaluate : 2.260 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 29 residues processed: 337 average time/residue: 1.1773 time to fit residues: 451.8203 Evaluate side-chains 318 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 289 time to evaluate : 2.343 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 18 residues processed: 11 average time/residue: 0.2195 time to fit residues: 7.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 133 optimal weight: 0.0270 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN C 260 GLN C 393 ASN C 687 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 18874 Z= 0.201 Angle : 0.632 15.569 25514 Z= 0.300 Chirality : 0.040 0.358 2862 Planarity : 0.005 0.105 3139 Dihedral : 11.329 176.537 2607 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.35 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.93 (0.18), residues: 2226 helix: 1.85 (0.14), residues: 1354 sheet: -0.62 (0.58), residues: 76 loop : -1.51 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 295 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 318 average time/residue: 1.2132 time to fit residues: 439.2159 Evaluate side-chains 318 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 289 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.2526 time to fit residues: 6.2047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN B 260 GLN B 393 ASN C 393 ASN C 687 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 18874 Z= 0.152 Angle : 0.622 15.699 25514 Z= 0.295 Chirality : 0.039 0.340 2862 Planarity : 0.004 0.077 3139 Dihedral : 11.147 178.306 2607 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.03 (0.18), residues: 2226 helix: 1.98 (0.14), residues: 1347 sheet: -0.48 (0.60), residues: 71 loop : -1.54 (0.22), residues: 808 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 306 time to evaluate : 2.326 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 329 average time/residue: 1.1746 time to fit residues: 440.0729 Evaluate side-chains 316 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 287 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.2208 time to fit residues: 6.0862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 198 optimal weight: 0.2980 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN B 260 GLN B 393 ASN B 687 ASN C 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.164 18874 Z= 0.187 Angle : 0.644 15.742 25514 Z= 0.310 Chirality : 0.039 0.338 2862 Planarity : 0.005 0.086 3139 Dihedral : 11.043 178.432 2607 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.05 (0.18), residues: 2226 helix: 2.00 (0.14), residues: 1346 sheet: -0.41 (0.60), residues: 71 loop : -1.54 (0.22), residues: 809 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 298 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 322 average time/residue: 1.2060 time to fit residues: 444.2847 Evaluate side-chains 313 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.3930 time to fit residues: 6.9747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 0.0000 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 135 optimal weight: 0.1980 chunk 107 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 676 ASN B 223 ASN B 260 GLN B 393 ASN C 652 ASN C 687 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 18874 Z= 0.176 Angle : 0.649 15.763 25514 Z= 0.307 Chirality : 0.038 0.327 2862 Planarity : 0.005 0.104 3139 Dihedral : 10.780 176.377 2607 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.10 (0.18), residues: 2226 helix: 2.04 (0.14), residues: 1350 sheet: -0.42 (0.60), residues: 71 loop : -1.53 (0.22), residues: 805 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 328 average time/residue: 1.1221 time to fit residues: 420.2465 Evaluate side-chains 318 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 298 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.1712 time to fit residues: 3.3186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 161 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN B 260 GLN B 393 ASN B 687 ASN C 687 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109213 restraints weight = 21669.209| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.98 r_work: 0.3181 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work: 0.3154 rms_B_bonded: 1.80 restraints_weight: 0.1250 r_work: 0.3139 rms_B_bonded: 1.87 restraints_weight: 0.0625 r_work: 0.3124 rms_B_bonded: 1.98 restraints_weight: 0.0312 r_work: 0.3108 rms_B_bonded: 2.11 restraints_weight: 0.0156 r_work: 0.3091 rms_B_bonded: 2.28 restraints_weight: 0.0078 r_work: 0.3073 rms_B_bonded: 2.49 restraints_weight: 0.0039 r_work: 0.3053 rms_B_bonded: 2.74 restraints_weight: 0.0020 r_work: 0.3032 rms_B_bonded: 3.03 restraints_weight: 0.0010 r_work: 0.3008 rms_B_bonded: 3.36 restraints_weight: 0.0005 r_work: 0.2983 rms_B_bonded: 3.75 restraints_weight: 0.0002 r_work: 0.2956 rms_B_bonded: 4.20 restraints_weight: 0.0001 r_work: 0.2928 rms_B_bonded: 4.72 restraints_weight: 0.0001 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.276 18874 Z= 0.206 Angle : 0.669 17.230 25514 Z= 0.322 Chirality : 0.040 0.331 2862 Planarity : 0.005 0.086 3139 Dihedral : 10.758 174.978 2607 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.06 (0.18), residues: 2226 helix: 2.03 (0.14), residues: 1339 sheet: -0.46 (0.61), residues: 71 loop : -1.54 (0.22), residues: 816 =============================================================================== Job complete usr+sys time: 7309.29 seconds wall clock time: 130 minutes 25.72 seconds (7825.72 seconds total)