Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 10:23:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3h_29699/10_2023/8g3h_29699_neut_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Co 1 6.85 5 Zn 1 6.06 5 P 1 5.49 5 S 26 5.16 5 C 4159 2.51 5 N 1125 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 6541 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6541 Unusual residues: {' ZN': 1, 'B12': 1} Classifications: {'peptide': 841, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 801, None: 2} Not linked: pdbres="THR A 877 " pdbres=" ZN A1201 " Not linked: pdbres=" ZN A1201 " pdbres="B12 A1202 " Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Unsupported chir.volume_sign: {'cros': 1} Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1673 SG CYS A 256 34.318 42.889 80.873 1.00 12.37 S ATOM 2190 SG CYS A 323 34.049 43.743 84.392 1.00 19.07 S Time building chain proxies: 4.13, per 1000 atoms: 0.63 Number of scatterers: 6541 At special positions: 0 Unit cell: (64.146, 90.8735, 112.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Co 1 26.99 S 26 16.00 P 1 15.00 O 1228 8.00 N 1125 7.00 C 4159 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 970.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 256 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 323 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 8 sheets defined 47.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.871A pdb=" N LYS A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.958A pdb=" N TYR A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.392A pdb=" N GLU A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 166 through 182 removed outlier: 3.630A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.716A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.682A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 6.119A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 4.352A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.509A pdb=" N ALA A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.076A pdb=" N LEU A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.711A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.690A pdb=" N GLU A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 3.883A pdb=" N LYS A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.870A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 580 through 597 removed outlier: 4.478A pdb=" N LYS A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 663 through 673 Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 699 through 713 removed outlier: 6.001A pdb=" N MET A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 738 removed outlier: 3.600A pdb=" N ALA A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Proline residue: A 737 - end of helix Processing helix chain 'A' and resid 761 through 773 removed outlier: 3.786A pdb=" N ILE A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 773 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 Processing helix chain 'A' and resid 808 through 823 removed outlier: 4.137A pdb=" N GLN A 812 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 841 No H-bonds generated for 'chain 'A' and resid 839 through 841' Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 858 through 869 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.135A pdb=" N PHE A 147 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 187 " --> pdb=" O GLY A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.689A pdb=" N PHE A 277 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 288 through 290 Processing sheet with id= E, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= F, first strand: chain 'A' and resid 369 through 372 removed outlier: 3.774A pdb=" N LEU A 569 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 409 through 412 removed outlier: 7.977A pdb=" N LEU A 412 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 441 " --> pdb=" O LEU A 412 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 748 through 751 removed outlier: 5.950A pdb=" N THR A 776 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A 751 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR A 778 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 230 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.33: 1750 1.33 - 1.50: 2012 1.50 - 1.67: 2846 1.67 - 1.84: 47 1.84 - 2.01: 4 Bond restraints: 6659 Sorted by residual: bond pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " ideal model delta sigma weight residual 1.426 1.651 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C15 B12 A1202 " pdb=" C53 B12 A1202 " ideal model delta sigma weight residual 1.500 1.685 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C4 B12 A1202 " pdb=" N21 B12 A1202 " ideal model delta sigma weight residual 1.416 1.235 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C49 B12 A1202 " pdb=" C50 B12 A1202 " ideal model delta sigma weight residual 1.510 1.337 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C5R B12 A1202 " pdb=" O8R B12 A1202 " ideal model delta sigma weight residual 1.432 1.267 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 83.37 - 102.24: 67 102.24 - 121.12: 7122 121.12 - 140.00: 1858 140.00 - 158.88: 0 158.88 - 177.76: 2 Bond angle restraints: 9049 Sorted by residual: angle pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" C ALA A 855 " ideal model delta sigma weight residual 110.24 83.37 26.87 1.30e+00 5.92e-01 4.27e+02 angle pdb=" C ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta sigma weight residual 109.64 137.87 -28.23 1.77e+00 3.19e-01 2.54e+02 angle pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" C VAL A 51 " ideal model delta sigma weight residual 108.17 123.43 -15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" C LEU A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 120.03 111.29 8.74 9.90e-01 1.02e+00 7.79e+01 angle pdb=" C18 B12 A1202 " pdb=" C19 B12 A1202 " pdb=" N24 B12 A1202 " ideal model delta sigma weight residual 120.00 94.26 25.74 3.00e+00 1.11e-01 7.36e+01 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3828 29.20 - 58.41: 191 58.41 - 87.61: 22 87.61 - 116.81: 1 116.81 - 146.02: 2 Dihedral angle restraints: 4044 sinusoidal: 1642 harmonic: 2402 Sorted by residual: dihedral pdb=" C ARG A 839 " pdb=" N ARG A 839 " pdb=" CA ARG A 839 " pdb=" CB ARG A 839 " ideal model delta harmonic sigma weight residual -122.60 -142.45 19.85 0 2.50e+00 1.60e-01 6.30e+01 dihedral pdb=" C ALA A 855 " pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta harmonic sigma weight residual -122.60 -139.40 16.80 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " pdb=" P B12 A1202 " pdb=" O4 B12 A1202 " ideal model delta sinusoidal sigma weight residual 60.00 -153.98 -146.02 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.110: 1034 1.110 - 2.220: 2 2.220 - 3.330: 2 3.330 - 4.441: 0 4.441 - 5.551: 1 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C12 B12 A1202 " pdb=" C11 B12 A1202 " pdb=" C46 B12 A1202 " pdb=" C47 B12 A1202 " both_signs ideal model delta sigma weight residual False -2.64 2.91 -5.55 2.00e-01 2.50e+01 7.70e+02 chirality pdb=" N21 B12 A1202 " pdb=" C1 B12 A1202 " pdb=" C4 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -3.05 0.08 -3.13 2.00e-01 2.50e+01 2.44e+02 chirality pdb=" N22 B12 A1202 " pdb=" C6 B12 A1202 " pdb=" C9 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -2.93 -0.18 -2.75 2.00e-01 2.50e+01 1.89e+02 ... (remaining 1036 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C35 B12 A1202 " -0.186 2.00e-02 2.50e+03 1.40e-01 2.94e+02 pdb=" C4 B12 A1202 " 0.093 2.00e-02 2.50e+03 pdb=" C5 B12 A1202 " 0.145 2.00e-02 2.50e+03 pdb=" C6 B12 A1202 " 0.038 2.00e-02 2.50e+03 pdb=" C7 B12 A1202 " 0.110 2.00e-02 2.50e+03 pdb=" N22 B12 A1202 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R B12 A1202 " 0.040 2.00e-02 2.50e+03 9.59e-02 2.76e+02 pdb=" C2B B12 A1202 " -0.137 2.00e-02 2.50e+03 pdb=" C4B B12 A1202 " -0.016 2.00e-02 2.50e+03 pdb=" C5B B12 A1202 " 0.036 2.00e-02 2.50e+03 pdb=" C5M B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C6B B12 A1202 " 0.060 2.00e-02 2.50e+03 pdb=" C6M B12 A1202 " -0.230 2.00e-02 2.50e+03 pdb=" C7B B12 A1202 " 0.088 2.00e-02 2.50e+03 pdb=" C8B B12 A1202 " 0.072 2.00e-02 2.50e+03 pdb=" C9B B12 A1202 " -0.006 2.00e-02 2.50e+03 pdb=" N1B B12 A1202 " 0.070 2.00e-02 2.50e+03 pdb=" N3B B12 A1202 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A1202 " 0.110 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C18 B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C19 B12 A1202 " -0.275 2.00e-02 2.50e+03 pdb=" N24 B12 A1202 " 0.071 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 685 2.76 - 3.30: 7181 3.30 - 3.83: 10965 3.83 - 4.37: 14137 4.37 - 4.90: 22386 Nonbonded interactions: 55354 Sorted by model distance: nonbonded pdb=" N ALA A 855 " pdb=" O ALA A 855 " model vdw 2.228 2.496 nonbonded pdb=" N GLY A 321 " pdb=" O GLY A 321 " model vdw 2.275 2.496 nonbonded pdb=" N MET A 803 " pdb=" O MET A 803 " model vdw 2.375 2.496 nonbonded pdb=" N ARG A 559 " pdb=" N GLU A 560 " model vdw 2.393 2.560 nonbonded pdb=" C TYR A 854 " pdb=" C ALA A 855 " model vdw 2.394 2.800 ... (remaining 55349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 11.720 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 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 : 0.016 0.225 6659 Z= 1.030 Angle : 2.317 28.234 9049 Z= 1.409 Chirality : 0.258 5.551 1039 Planarity : 0.017 0.160 1180 Dihedral : 17.251 146.016 2506 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.37 % Allowed : 14.61 % Favored : 81.02 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.24), residues: 839 helix: -2.85 (0.19), residues: 387 sheet: -1.65 (0.76), residues: 47 loop : -2.56 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 6 residues processed: 168 average time/residue: 0.2572 time to fit residues: 53.5688 Evaluate side-chains 100 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0820 time to fit residues: 1.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 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 194 GLN A 198 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6659 Z= 0.314 Angle : 1.151 31.526 9049 Z= 0.506 Chirality : 0.094 2.388 1039 Planarity : 0.006 0.054 1180 Dihedral : 11.273 138.020 967 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.92 % Allowed : 17.02 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.26), residues: 839 helix: -1.29 (0.23), residues: 382 sheet: -1.84 (0.64), residues: 60 loop : -1.84 (0.30), residues: 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 124 average time/residue: 0.1838 time to fit residues: 31.0893 Evaluate side-chains 96 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0765 time to fit residues: 2.7050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6659 Z= 0.262 Angle : 1.058 31.030 9049 Z= 0.449 Chirality : 0.092 2.402 1039 Planarity : 0.005 0.058 1180 Dihedral : 10.319 135.863 967 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.36 % Allowed : 20.93 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.27), residues: 839 helix: -0.70 (0.24), residues: 379 sheet: -2.32 (0.52), residues: 88 loop : -1.56 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 0.1428 time to fit residues: 20.0508 Evaluate side-chains 85 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0650 time to fit residues: 1.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6659 Z= 0.255 Angle : 1.029 31.075 9049 Z= 0.432 Chirality : 0.090 2.392 1039 Planarity : 0.005 0.062 1180 Dihedral : 9.836 132.234 967 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.71 % Allowed : 20.63 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.27), residues: 839 helix: -0.54 (0.24), residues: 387 sheet: -1.98 (0.68), residues: 55 loop : -1.62 (0.30), residues: 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 103 average time/residue: 0.1594 time to fit residues: 23.4281 Evaluate side-chains 85 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0732 time to fit residues: 1.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 1 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6659 Z= 0.216 Angle : 1.000 30.918 9049 Z= 0.413 Chirality : 0.090 2.408 1039 Planarity : 0.005 0.065 1180 Dihedral : 9.409 129.764 967 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 22.14 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.28), residues: 839 helix: -0.30 (0.25), residues: 390 sheet: -1.69 (0.65), residues: 65 loop : -1.52 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 101 average time/residue: 0.1589 time to fit residues: 23.0123 Evaluate side-chains 83 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0675 time to fit residues: 1.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6659 Z= 0.258 Angle : 1.011 30.994 9049 Z= 0.425 Chirality : 0.090 2.393 1039 Planarity : 0.005 0.064 1180 Dihedral : 9.338 126.514 967 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.56 % Allowed : 22.14 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 839 helix: -0.37 (0.25), residues: 378 sheet: -1.92 (0.68), residues: 55 loop : -1.53 (0.30), residues: 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 98 average time/residue: 0.1752 time to fit residues: 23.9103 Evaluate side-chains 91 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0814 time to fit residues: 1.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 49 optimal weight: 0.0470 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6659 Z= 0.207 Angle : 0.988 30.858 9049 Z= 0.411 Chirality : 0.089 2.409 1039 Planarity : 0.005 0.066 1180 Dihedral : 9.023 122.643 967 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 22.89 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.28), residues: 839 helix: -0.30 (0.25), residues: 384 sheet: -2.11 (0.62), residues: 67 loop : -1.52 (0.30), residues: 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 0.1811 time to fit residues: 25.9124 Evaluate side-chains 90 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0748 time to fit residues: 1.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.0370 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6659 Z= 0.281 Angle : 1.039 31.229 9049 Z= 0.436 Chirality : 0.090 2.390 1039 Planarity : 0.005 0.065 1180 Dihedral : 9.116 122.138 967 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.20 % Allowed : 23.80 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.28), residues: 839 helix: -0.40 (0.25), residues: 379 sheet: -2.28 (0.65), residues: 60 loop : -1.56 (0.30), residues: 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1670 time to fit residues: 22.1323 Evaluate side-chains 87 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0729 time to fit residues: 1.5230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6659 Z= 0.272 Angle : 1.046 31.341 9049 Z= 0.441 Chirality : 0.090 2.398 1039 Planarity : 0.005 0.063 1180 Dihedral : 9.067 119.626 967 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.05 % Allowed : 24.40 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.27), residues: 839 helix: -0.56 (0.24), residues: 389 sheet: -2.22 (0.65), residues: 55 loop : -1.63 (0.31), residues: 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.1638 time to fit residues: 19.7453 Evaluate side-chains 84 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0777 time to fit residues: 1.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6659 Z= 0.251 Angle : 1.031 31.321 9049 Z= 0.433 Chirality : 0.089 2.397 1039 Planarity : 0.005 0.064 1180 Dihedral : 8.973 116.565 967 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.75 % Allowed : 25.30 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.28), residues: 839 helix: -0.52 (0.25), residues: 391 sheet: -2.23 (0.64), residues: 60 loop : -1.59 (0.31), residues: 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 0.1628 time to fit residues: 19.0924 Evaluate side-chains 78 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0941 time to fit residues: 1.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.221937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.201076 restraints weight = 8618.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.205001 restraints weight = 5525.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.207817 restraints weight = 3874.613| |-----------------------------------------------------------------------------| r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6659 Z= 0.281 Angle : 1.048 31.506 9049 Z= 0.444 Chirality : 0.090 2.395 1039 Planarity : 0.005 0.064 1180 Dihedral : 9.049 115.012 967 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.45 % Allowed : 26.36 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.28), residues: 839 helix: -0.53 (0.25), residues: 393 sheet: -2.23 (0.64), residues: 55 loop : -1.53 (0.32), residues: 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.82 seconds wall clock time: 33 minutes 25.35 seconds (2005.35 seconds total)