Starting phenix.real_space_refine on Sat Dec 9 04:16:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syn_40885/12_2023/8syn_40885.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6487 2.51 5 N 1695 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10069 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6474 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175} Chain: "C" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.50, per 1000 atoms: 0.55 Number of scatterers: 10069 At special positions: 0 Unit cell: (78.6176, 108.365, 172.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1825 8.00 N 1695 7.00 C 6487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 53.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.805A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.731A pdb=" N LEU A 218 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 254 removed outlier: 3.628A pdb=" N ASP A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.647A pdb=" N ILE A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 310 through 323 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 350 through 365 removed outlier: 4.224A pdb=" N LYS A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.004A pdb=" N TRP A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.666A pdb=" N ASN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.666A pdb=" N GLU A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.885A pdb=" N LEU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.569A pdb=" N VAL A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.879A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.805A pdb=" N GLU A 540 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.689A pdb=" N PHE A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 removed outlier: 4.008A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.607A pdb=" N GLU A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.773A pdb=" N MET A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 667 through 689 Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.736A pdb=" N ALA A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 768 through 784 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.587A pdb=" N ARG A 819 " --> pdb=" O ASP A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 881 Processing helix chain 'A' and resid 883 through 901 Processing helix chain 'A' and resid 906 through 923 removed outlier: 3.633A pdb=" N HIS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.602A pdb=" N LYS B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.784A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.862A pdb=" N ALA C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.589A pdb=" N ARG B 180 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.530A pdb=" N LYS B 85 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE B 116 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 87 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 134 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 117 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 79 removed outlier: 5.878A pdb=" N GLN C 70 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 47 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 72 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 39 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.726A pdb=" N LEU C 177 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 239 removed outlier: 6.962A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 272 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1761 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: 3.53 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3228 1.34 - 1.46: 1988 1.46 - 1.58: 4977 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10283 Sorted by residual: bond pdb=" CG1 ILE A 712 " pdb=" CD1 ILE A 712 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.09e+00 bond pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta sigma weight residual 1.463 1.478 -0.015 1.20e-02 6.94e+03 1.55e+00 bond pdb=" C THR A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" SD MET A 395 " pdb=" CE MET A 395 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 10278 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.53: 185 105.53 - 112.64: 5561 112.64 - 119.76: 3273 119.76 - 126.87: 4782 126.87 - 133.98: 119 Bond angle restraints: 13920 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.45 115.92 -5.47 7.80e-01 1.64e+00 4.91e+01 angle pdb=" C ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 114.00 106.87 7.13 1.31e+00 5.83e-01 2.96e+01 angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CB LYS A 602 " pdb=" CG LYS A 602 " pdb=" CD LYS A 602 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB MET A 533 " pdb=" CG MET A 533 " pdb=" SD MET A 533 " ideal model delta sigma weight residual 112.70 102.95 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 13915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5653 17.65 - 35.31: 473 35.31 - 52.96: 67 52.96 - 70.61: 8 70.61 - 88.27: 9 Dihedral angle restraints: 6210 sinusoidal: 2513 harmonic: 3697 Sorted by residual: dihedral pdb=" CA CYS A 737 " pdb=" C CYS A 737 " pdb=" N LEU A 738 " pdb=" CA LEU A 738 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLY C 148 " pdb=" C GLY C 148 " pdb=" N LYS C 149 " pdb=" CA LYS C 149 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 535 " pdb=" C PRO A 535 " pdb=" N ASP A 536 " pdb=" CA ASP A 536 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1131 0.040 - 0.080: 318 0.080 - 0.120: 130 0.120 - 0.160: 23 0.160 - 0.199: 1 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA MET A 533 " pdb=" N MET A 533 " pdb=" C MET A 533 " pdb=" CB MET A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" C PRO A 535 " pdb=" CB PRO A 535 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1600 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO A 385 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 821 " -0.019 2.00e-02 2.50e+03 1.65e-02 5.45e+00 pdb=" CG TYR A 821 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 821 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 821 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 821 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 821 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 821 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 534 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 535 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.027 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 453 2.73 - 3.27: 10483 3.27 - 3.81: 16677 3.81 - 4.36: 19664 4.36 - 4.90: 33992 Nonbonded interactions: 81269 Sorted by model distance: nonbonded pdb=" NZ LYS B 25 " pdb=" O ASP B 174 " model vdw 2.182 2.520 nonbonded pdb=" OH TYR A 387 " pdb=" OH TYR A 391 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU A 297 " pdb=" NH2 ARG A 318 " model vdw 2.215 2.520 nonbonded pdb=" O PRO A 34 " pdb=" NZ LYS B 34 " model vdw 2.217 2.520 nonbonded pdb=" O PHE A 656 " pdb=" OG SER A 660 " model vdw 2.232 2.440 ... (remaining 81264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.550 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: 5.900 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.670 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 0.004 0.069 10283 Z= 0.253 Angle : 0.625 9.753 13920 Z= 0.341 Chirality : 0.044 0.199 1603 Planarity : 0.005 0.083 1761 Dihedral : 13.189 88.268 3800 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.88 (0.25), residues: 1237 helix: 1.23 (0.21), residues: 597 sheet: 0.19 (0.38), residues: 197 loop : 0.04 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.014 0.001 HIS A 596 PHE 0.024 0.002 PHE C 93 TYR 0.041 0.002 TYR A 821 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 1.1160 time to fit residues: 317.5253 Evaluate side-chains 239 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 72 optimal weight: 40.0000 chunk 113 optimal weight: 0.5980 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS A 778 ASN A 911 GLN C 115 ASN C 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10283 Z= 0.215 Angle : 0.604 7.559 13920 Z= 0.307 Chirality : 0.043 0.144 1603 Planarity : 0.004 0.059 1761 Dihedral : 4.240 19.215 1338 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 11.42 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.30 (0.25), residues: 1237 helix: 1.61 (0.21), residues: 624 sheet: 0.51 (0.39), residues: 195 loop : 0.03 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 810 HIS 0.009 0.001 HIS B 90 PHE 0.024 0.002 PHE A 796 TYR 0.026 0.002 TYR B 73 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 253 average time/residue: 1.0318 time to fit residues: 283.5124 Evaluate side-chains 237 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.7434 time to fit residues: 5.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN A 727 HIS B 170 GLN C 115 ASN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10283 Z= 0.294 Angle : 0.608 9.473 13920 Z= 0.309 Chirality : 0.044 0.154 1603 Planarity : 0.004 0.053 1761 Dihedral : 4.276 19.000 1338 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.74 % Allowed : 14.96 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.39 (0.25), residues: 1237 helix: 1.74 (0.21), residues: 622 sheet: 0.44 (0.39), residues: 195 loop : 0.05 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 810 HIS 0.010 0.001 HIS A 596 PHE 0.037 0.002 PHE A 796 TYR 0.020 0.002 TYR A 821 ARG 0.005 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 254 average time/residue: 1.0473 time to fit residues: 288.9910 Evaluate side-chains 250 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 237 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 4 residues processed: 9 average time/residue: 0.4514 time to fit residues: 6.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN A 727 HIS B 128 HIS C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10283 Z= 0.343 Angle : 0.631 13.845 13920 Z= 0.322 Chirality : 0.045 0.173 1603 Planarity : 0.004 0.050 1761 Dihedral : 4.332 18.405 1338 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.57 % Allowed : 17.26 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.34 (0.25), residues: 1237 helix: 1.67 (0.21), residues: 623 sheet: 0.43 (0.39), residues: 195 loop : 0.05 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 490 HIS 0.009 0.001 HIS A 596 PHE 0.044 0.002 PHE A 796 TYR 0.034 0.002 TYR B 73 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 260 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 270 average time/residue: 1.3043 time to fit residues: 379.9757 Evaluate side-chains 264 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 0.4166 time to fit residues: 6.0866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10283 Z= 0.328 Angle : 0.645 10.317 13920 Z= 0.328 Chirality : 0.045 0.166 1603 Planarity : 0.004 0.048 1761 Dihedral : 4.363 18.549 1338 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.04 % Allowed : 19.12 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.26 (0.25), residues: 1237 helix: 1.63 (0.21), residues: 624 sheet: 0.33 (0.39), residues: 195 loop : 0.01 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 490 HIS 0.004 0.001 HIS A 462 PHE 0.034 0.002 PHE A 796 TYR 0.036 0.002 TYR B 73 ARG 0.009 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 254 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 263 average time/residue: 1.1316 time to fit residues: 321.7781 Evaluate side-chains 253 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 4 residues processed: 11 average time/residue: 0.4778 time to fit residues: 7.7467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10283 Z= 0.264 Angle : 0.628 9.979 13920 Z= 0.318 Chirality : 0.044 0.153 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.296 20.660 1338 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.57 % Allowed : 19.56 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.37 (0.25), residues: 1237 helix: 1.73 (0.21), residues: 621 sheet: 0.41 (0.39), residues: 195 loop : 0.04 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.004 0.001 HIS A 462 PHE 0.031 0.002 PHE A 796 TYR 0.029 0.002 TYR B 73 ARG 0.005 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 266 average time/residue: 1.1744 time to fit residues: 336.4094 Evaluate side-chains 253 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 0.4823 time to fit residues: 5.5923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 0.0010 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 234 ASN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10283 Z= 0.266 Angle : 0.671 15.304 13920 Z= 0.332 Chirality : 0.044 0.170 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.285 18.286 1338 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.57 % Allowed : 21.15 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.30 (0.25), residues: 1237 helix: 1.66 (0.21), residues: 622 sheet: 0.38 (0.39), residues: 195 loop : 0.00 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.004 0.001 HIS A 462 PHE 0.053 0.002 PHE A 796 TYR 0.035 0.002 TYR B 73 ARG 0.007 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 1.143 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 262 average time/residue: 1.1355 time to fit residues: 321.7514 Evaluate side-chains 251 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.4717 time to fit residues: 6.1444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 40.0000 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10283 Z= 0.275 Angle : 0.693 13.968 13920 Z= 0.344 Chirality : 0.045 0.161 1603 Planarity : 0.004 0.046 1761 Dihedral : 4.325 17.776 1338 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.95 % Allowed : 22.74 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.24 (0.25), residues: 1237 helix: 1.57 (0.21), residues: 622 sheet: 0.34 (0.38), residues: 195 loop : 0.07 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 490 HIS 0.015 0.001 HIS A 596 PHE 0.049 0.002 PHE A 796 TYR 0.028 0.002 TYR B 73 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 252 average time/residue: 1.1290 time to fit residues: 307.1342 Evaluate side-chains 254 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 239 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.3193 time to fit residues: 4.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10283 Z= 0.341 Angle : 0.729 13.475 13920 Z= 0.360 Chirality : 0.046 0.173 1603 Planarity : 0.004 0.047 1761 Dihedral : 4.406 17.637 1338 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.86 % Allowed : 23.54 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.08 (0.24), residues: 1237 helix: 1.41 (0.21), residues: 623 sheet: 0.27 (0.38), residues: 195 loop : 0.02 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.005 0.001 HIS A 596 PHE 0.046 0.002 PHE A 796 TYR 0.035 0.002 TYR B 73 ARG 0.009 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 252 average time/residue: 1.1425 time to fit residues: 310.3129 Evaluate side-chains 249 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.1142 time to fit residues: 2.7276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 727 HIS A 778 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 10283 Z= 0.358 Angle : 0.750 13.231 13920 Z= 0.371 Chirality : 0.047 0.204 1603 Planarity : 0.005 0.048 1761 Dihedral : 4.486 17.575 1338 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.33 % Allowed : 24.42 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.04 (0.24), residues: 1237 helix: 1.33 (0.21), residues: 624 sheet: 0.34 (0.40), residues: 184 loop : 0.05 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 199 HIS 0.004 0.001 HIS A 462 PHE 0.043 0.002 PHE A 796 TYR 0.032 0.002 TYR B 73 ARG 0.006 0.001 ARG A 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 237 average time/residue: 1.1617 time to fit residues: 298.9718 Evaluate side-chains 236 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 225 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1226 time to fit residues: 2.4710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS A 596 HIS A 727 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 233 GLN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.148315 restraints weight = 15678.279| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.45 r_work: 0.3742 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10283 Z= 0.263 Angle : 0.746 13.622 13920 Z= 0.367 Chirality : 0.046 0.330 1603 Planarity : 0.004 0.046 1761 Dihedral : 4.454 17.308 1338 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.15 % Allowed : 24.78 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.25), residues: 1237 helix: 1.40 (0.21), residues: 628 sheet: 0.22 (0.38), residues: 194 loop : 0.01 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 490 HIS 0.004 0.001 HIS A 462 PHE 0.046 0.002 PHE A 796 TYR 0.026 0.002 TYR B 73 ARG 0.005 0.000 ARG A 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4868.39 seconds wall clock time: 86 minutes 52.19 seconds (5212.19 seconds total)