Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 20:16:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/04_2023/6xmg_22258.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 154 5.49 5 S 11 5.16 5 C 4674 2.51 5 N 1553 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 17": "NH1" <-> "NH2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5081 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 38, 'TRANS': 599} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2772 Classifications: {'RNA': 130} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 56} Link IDs: {'rna2p': 15, 'rna3p': 114} Chain breaks: 1 Chain: "E" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 507 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4654 SG CYS A 714 51.688 83.830 49.919 1.00352.65 S Time building chain proxies: 5.15, per 1000 atoms: 0.62 Number of scatterers: 8361 At special positions: 0 Unit cell: (106.05, 94.5, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 11 16.00 P 154 15.00 O 1968 8.00 N 1553 7.00 C 4674 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: 4.00 Conformation dependent library (CDL) restraints added in 876.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 49.4% alpha, 5.8% beta 43 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.637A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.754A pdb=" N TRP A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.970A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.622A pdb=" N ARG A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.818A pdb=" N SER A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.518A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 200 removed outlier: 3.892A pdb=" N GLN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.540A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.565A pdb=" N LYS A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.669A pdb=" N THR A 434 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.741A pdb=" N LEU A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.723A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 569 through 595 removed outlier: 3.804A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 644 removed outlier: 3.593A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.660A pdb=" N ARG A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 4.009A pdb=" N ARG A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.630A pdb=" N TRP A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.685A pdb=" N ARG A 26 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 450 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 438 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 441 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.564A pdb=" N VAL A 653 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 652 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524 removed outlier: 6.725A pdb=" N ALA A 521 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 532 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 523 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 530 " --> pdb=" O PHE A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 195 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1025 1.31 - 1.43: 3323 1.43 - 1.56: 4192 1.56 - 1.69: 305 1.69 - 1.81: 16 Bond restraints: 8861 Sorted by residual: bond pdb=" C ARG A 675 " pdb=" O ARG A 675 " ideal model delta sigma weight residual 1.233 1.180 0.052 1.09e-02 8.42e+03 2.31e+01 bond pdb=" C ARG A 675 " pdb=" N VAL A 676 " ideal model delta sigma weight residual 1.332 1.305 0.026 1.36e-02 5.41e+03 3.79e+00 bond pdb=" CA ILE A 766 " pdb=" CB ILE A 766 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.68e+00 bond pdb=" N ARG A 675 " pdb=" CA ARG A 675 " ideal model delta sigma weight residual 1.463 1.482 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" N LYS A 551 " pdb=" CA LYS A 551 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.72: 1046 106.72 - 113.53: 4904 113.53 - 120.34: 3388 120.34 - 127.15: 3016 127.15 - 133.96: 360 Bond angle restraints: 12714 Sorted by residual: angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" CB PRO A 229 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C3' A C 113 " pdb=" O3' A C 113 " pdb=" P A C 114 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" N GLN A 552 " pdb=" CA GLN A 552 " pdb=" C GLN A 552 " ideal model delta sigma weight residual 107.73 112.27 -4.54 1.34e+00 5.57e-01 1.15e+01 angle pdb=" C LEU A 203 " pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 122.89 119.38 3.51 1.12e+00 7.97e-01 9.84e+00 angle pdb=" C LYS A 610 " pdb=" CA LYS A 610 " pdb=" CB LYS A 610 " ideal model delta sigma weight residual 110.88 115.55 -4.67 1.57e+00 4.06e-01 8.86e+00 ... (remaining 12709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 4862 35.70 - 71.39: 141 71.39 - 107.09: 15 107.09 - 142.78: 4 142.78 - 178.48: 5 Dihedral angle restraints: 5027 sinusoidal: 3163 harmonic: 1864 Sorted by residual: dihedral pdb=" O4' U C 55 " pdb=" C1' U C 55 " pdb=" N1 U C 55 " pdb=" C2 U C 55 " ideal model delta sinusoidal sigma weight residual 200.00 44.85 155.15 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' U C 45 " pdb=" C1' U C 45 " pdb=" N1 U C 45 " pdb=" C2 U C 45 " ideal model delta sinusoidal sigma weight residual 232.00 57.13 174.87 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA GLU A 21 " pdb=" C GLU A 21 " pdb=" N ARG A 22 " pdb=" CA ARG A 22 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1346 0.046 - 0.093: 128 0.093 - 0.139: 19 0.139 - 0.185: 3 0.185 - 0.232: 2 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA PRO A 229 " pdb=" N PRO A 229 " pdb=" C PRO A 229 " pdb=" CB PRO A 229 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' A C 113 " pdb=" C4' A C 113 " pdb=" O3' A C 113 " pdb=" C2' A C 113 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A C 76 " pdb=" C4' A C 76 " pdb=" O3' A C 76 " pdb=" C2' A C 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1495 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 675 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ARG A 675 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 675 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 676 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 427 " -0.014 2.00e-02 2.50e+03 1.38e-02 3.83e+00 pdb=" CG TYR A 427 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 427 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 427 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 427 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 427 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 156 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 157 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.023 5.00e-02 4.00e+02 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 658 2.73 - 3.27: 8128 3.27 - 3.81: 15463 3.81 - 4.36: 19635 4.36 - 4.90: 27945 Nonbonded interactions: 71829 Sorted by model distance: nonbonded pdb=" O CYS A 714 " pdb="ZN ZN A 801 " model vdw 2.187 2.230 nonbonded pdb=" O ARG A 685 " pdb=" OG1 THR A 689 " model vdw 2.276 2.440 nonbonded pdb=" O2' U C 13 " pdb=" OP2 G C 22 " model vdw 2.277 2.440 nonbonded pdb=" OG1 THR A 466 " pdb=" OE1 GLU A 468 " model vdw 2.293 2.440 nonbonded pdb=" NH2 ARG A 26 " pdb=" O2' C C 111 " model vdw 2.299 2.520 ... (remaining 71824 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: 0.960 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: 2.470 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 29.780 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.002 0.052 8861 Z= 0.130 Angle : 0.526 7.443 12714 Z= 0.329 Chirality : 0.029 0.232 1498 Planarity : 0.004 0.041 1088 Dihedral : 16.060 178.481 3809 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.33), residues: 628 helix: -0.24 (0.31), residues: 275 sheet: -3.40 (0.70), residues: 40 loop : -2.07 (0.34), residues: 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.749 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2948 time to fit residues: 12.3391 Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8861 Z= 0.218 Angle : 0.661 6.202 12714 Z= 0.334 Chirality : 0.037 0.197 1498 Planarity : 0.005 0.039 1088 Dihedral : 16.244 179.734 2551 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.33), residues: 628 helix: 0.14 (0.30), residues: 277 sheet: -2.69 (0.90), residues: 30 loop : -1.93 (0.34), residues: 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.3750 time to fit residues: 14.4299 Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 30.0000 chunk 21 optimal weight: 40.0000 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 8861 Z= 0.380 Angle : 0.913 10.027 12714 Z= 0.467 Chirality : 0.045 0.205 1498 Planarity : 0.007 0.046 1088 Dihedral : 18.415 177.625 2551 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 49.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 0.40 % 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: -2.48 (0.31), residues: 628 helix: -0.39 (0.29), residues: 281 sheet: -4.11 (0.64), residues: 40 loop : -2.56 (0.31), residues: 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.4219 time to fit residues: 13.0415 Evaluate side-chains 20 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3899 time to fit residues: 1.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 8861 Z= 0.295 Angle : 0.784 6.490 12714 Z= 0.404 Chirality : 0.042 0.250 1498 Planarity : 0.006 0.071 1088 Dihedral : 18.801 179.229 2551 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 42.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 0.20 % 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: -2.29 (0.31), residues: 628 helix: -0.30 (0.30), residues: 272 sheet: -3.54 (0.81), residues: 31 loop : -2.45 (0.32), residues: 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.4128 time to fit residues: 14.1481 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8861 Z= 0.220 Angle : 0.705 10.795 12714 Z= 0.362 Chirality : 0.039 0.266 1498 Planarity : 0.005 0.067 1088 Dihedral : 18.636 179.950 2551 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 0.20 % 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: -2.00 (0.32), residues: 628 helix: -0.01 (0.31), residues: 273 sheet: -3.21 (0.86), residues: 29 loop : -2.38 (0.32), residues: 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.4287 time to fit residues: 15.6229 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 0.0010 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8861 Z= 0.226 Angle : 0.703 10.208 12714 Z= 0.361 Chirality : 0.039 0.269 1498 Planarity : 0.005 0.053 1088 Dihedral : 18.728 179.540 2551 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 38.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.32), residues: 628 helix: -0.02 (0.31), residues: 274 sheet: -3.61 (0.84), residues: 31 loop : -2.36 (0.33), residues: 323 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.4392 time to fit residues: 14.9299 Evaluate side-chains 16 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8861 Z= 0.244 Angle : 0.726 9.636 12714 Z= 0.375 Chirality : 0.040 0.272 1498 Planarity : 0.006 0.049 1088 Dihedral : 18.964 179.882 2551 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 42.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.33), residues: 628 helix: -0.03 (0.32), residues: 272 sheet: -3.45 (0.85), residues: 30 loop : -2.32 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3878 time to fit residues: 12.6652 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.0670 overall best weight: 4.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8861 Z= 0.204 Angle : 0.685 10.110 12714 Z= 0.354 Chirality : 0.039 0.272 1498 Planarity : 0.005 0.054 1088 Dihedral : 18.846 179.936 2551 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.20 % 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 (0.33), residues: 628 helix: 0.00 (0.31), residues: 273 sheet: -3.30 (0.84), residues: 29 loop : -2.34 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.3638 time to fit residues: 12.4535 Evaluate side-chains 19 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8861 Z= 0.216 Angle : 0.692 9.940 12714 Z= 0.357 Chirality : 0.038 0.269 1498 Planarity : 0.005 0.054 1088 Dihedral : 18.867 179.666 2551 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 39.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer Outliers : 0.20 % 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: -1.91 (0.33), residues: 628 helix: 0.07 (0.31), residues: 273 sheet: -3.43 (0.83), residues: 29 loop : -2.32 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.3699 time to fit residues: 12.2906 Evaluate side-chains 17 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 8861 Z= 0.231 Angle : 0.710 10.490 12714 Z= 0.365 Chirality : 0.039 0.266 1498 Planarity : 0.006 0.052 1088 Dihedral : 18.941 179.962 2551 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 40.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.20 % 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: -1.93 (0.33), residues: 628 helix: 0.06 (0.31), residues: 273 sheet: -3.51 (0.82), residues: 29 loop : -2.33 (0.33), residues: 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.3585 time to fit residues: 11.9558 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.042717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.034076 restraints weight = 138331.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034803 restraints weight = 109165.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.035283 restraints weight = 91250.140| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8861 Z= 0.252 Angle : 0.747 10.725 12714 Z= 0.385 Chirality : 0.041 0.259 1498 Planarity : 0.006 0.054 1088 Dihedral : 19.165 179.941 2551 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 46.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer Outliers : 0.20 % 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: -2.08 (0.33), residues: 628 helix: -0.06 (0.31), residues: 272 sheet: -3.69 (0.73), residues: 34 loop : -2.36 (0.33), residues: 322 =============================================================================== Job complete usr+sys time: 1275.69 seconds wall clock time: 24 minutes 43.40 seconds (1483.40 seconds total)