Starting phenix.real_space_refine on Fri Dec 8 12:14:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/12_2023/6xmg_22258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/12_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_22258/12_2023/6xmg_22258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/12_2023/6xmg_22258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/12_2023/6xmg_22258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmg_22258/12_2023/6xmg_22258.pdb" } resolution = 4.8 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= 0.002 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.17, 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: 4.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.99 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: 4.46 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: 5013 35.70 - 71.39: 341 71.39 - 107.09: 54 107.09 - 142.78: 4 142.78 - 178.48: 5 Dihedral angle restraints: 5417 sinusoidal: 3553 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 5414 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: 0.330 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: 2.140 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.330 Find NCS groups from input model: 0.180 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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 : 20.811 178.481 4199 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.002 0.001 HIS A 159 PHE 0.010 0.001 PHE A 398 TYR 0.033 0.002 TYR A 427 ARG 0.007 0.001 ARG A 638 *********************** 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 : 0.783 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2986 time to fit residues: 12.5411 Evaluate side-chains 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8697 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.1950 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= 0.208 Angle : 0.659 6.501 12714 Z= 0.332 Chirality : 0.037 0.196 1498 Planarity : 0.005 0.042 1088 Dihedral : 22.396 179.856 2941 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: -1.50 (0.33), residues: 628 helix: 0.20 (0.30), residues: 277 sheet: -2.72 (0.90), residues: 30 loop : -1.95 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 724 HIS 0.002 0.001 HIS A 572 PHE 0.015 0.002 PHE A 756 TYR 0.018 0.002 TYR A 427 ARG 0.020 0.001 ARG A 177 *********************** 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 : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.3762 time to fit residues: 14.6121 Evaluate side-chains 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9445 ------------------------------------------------------------------------------- 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: 40.0000 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 19 optimal weight: 0.0870 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 53 optimal weight: 4.9990 overall best weight: 5.4170 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8861 Z= 0.231 Angle : 0.679 5.705 12714 Z= 0.349 Chirality : 0.038 0.186 1498 Planarity : 0.005 0.044 1088 Dihedral : 22.954 179.412 2941 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 31.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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: -1.84 (0.33), residues: 628 helix: 0.03 (0.30), residues: 286 sheet: -3.52 (0.72), residues: 40 loop : -2.16 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 724 HIS 0.004 0.001 HIS A 572 PHE 0.018 0.002 PHE A 102 TYR 0.016 0.002 TYR A 427 ARG 0.007 0.001 ARG A 683 *********************** 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 29 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4047 time to fit residues: 14.8438 Evaluate side-chains 24 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9345 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 overall best weight: 6.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8861 Z= 0.250 Angle : 0.701 5.985 12714 Z= 0.360 Chirality : 0.039 0.227 1498 Planarity : 0.005 0.054 1088 Dihedral : 23.184 179.815 2941 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 33.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -1.79 (0.32), residues: 628 helix: 0.21 (0.31), residues: 278 sheet: -2.83 (0.87), residues: 29 loop : -2.40 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.006 0.002 HIS A 624 PHE 0.019 0.002 PHE A 756 TYR 0.016 0.002 TYR A 175 ARG 0.006 0.001 ARG A 508 *********************** 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 28 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.3587 time to fit residues: 13.0714 Evaluate side-chains 20 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8839 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- 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 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: 0.7863 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8861 Z= 0.285 Angle : 0.761 9.939 12714 Z= 0.390 Chirality : 0.041 0.265 1498 Planarity : 0.006 0.061 1088 Dihedral : 23.611 179.935 2941 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 42.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -2.12 (0.31), residues: 628 helix: -0.08 (0.30), residues: 278 sheet: -3.23 (0.84), residues: 30 loop : -2.52 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 82 HIS 0.006 0.002 HIS A 442 PHE 0.017 0.003 PHE A 756 TYR 0.017 0.002 TYR A 393 ARG 0.010 0.001 ARG A 674 *********************** 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 26 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3811 time to fit residues: 12.8075 Evaluate side-chains 20 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8931 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 62 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 ** 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: 0.7861 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8861 Z= 0.272 Angle : 0.749 9.194 12714 Z= 0.387 Chirality : 0.040 0.272 1498 Planarity : 0.006 0.049 1088 Dihedral : 23.792 179.968 2941 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 40.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 (0.32), residues: 628 helix: 0.06 (0.31), residues: 272 sheet: -3.42 (0.83), residues: 30 loop : -2.32 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 82 HIS 0.009 0.002 HIS A 681 PHE 0.026 0.003 PHE A 733 TYR 0.017 0.002 TYR A 393 ARG 0.009 0.001 ARG A 147 *********************** 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 : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3788 time to fit residues: 13.2515 Evaluate side-chains 18 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0053 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8861 Z= 0.189 Angle : 0.667 8.655 12714 Z= 0.345 Chirality : 0.038 0.279 1498 Planarity : 0.005 0.043 1088 Dihedral : 23.612 179.506 2941 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 34.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % 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: -1.82 (0.33), residues: 628 helix: 0.17 (0.31), residues: 273 sheet: -3.43 (0.84), residues: 30 loop : -2.28 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 82 HIS 0.005 0.001 HIS A 179 PHE 0.014 0.002 PHE A 533 TYR 0.014 0.002 TYR A 175 ARG 0.004 0.001 ARG A 674 *********************** 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 27 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.3290 time to fit residues: 11.9674 Evaluate side-chains 19 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9568 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 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: 0.7980 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 563 GLN ** 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: 0.7849 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8861 Z= 0.245 Angle : 0.720 8.796 12714 Z= 0.370 Chirality : 0.039 0.275 1498 Planarity : 0.006 0.099 1088 Dihedral : 23.711 179.610 2941 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 42.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.33), residues: 628 helix: 0.08 (0.32), residues: 273 sheet: -3.45 (0.84), residues: 30 loop : -2.34 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 82 HIS 0.005 0.002 HIS A 442 PHE 0.015 0.002 PHE A 756 TYR 0.017 0.002 TYR A 393 ARG 0.009 0.001 ARG A 674 *********************** 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 25 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3349 time to fit residues: 11.2616 Evaluate side-chains 19 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9302 ------------------------------------------------------------------------------- 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: 10.0000 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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: 0.7886 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8861 Z= 0.304 Angle : 0.801 9.685 12714 Z= 0.414 Chirality : 0.043 0.274 1498 Planarity : 0.007 0.083 1088 Dihedral : 24.012 179.319 2941 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 49.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.20 % Allowed : 1.21 % Favored : 98.59 % 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: -2.26 (0.32), residues: 628 helix: -0.29 (0.31), residues: 273 sheet: -3.72 (0.75), residues: 35 loop : -2.39 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 82 HIS 0.006 0.002 HIS A 442 PHE 0.018 0.003 PHE A 67 TYR 0.021 0.002 TYR A 393 ARG 0.006 0.001 ARG A 627 *********************** 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 : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.3574 time to fit residues: 12.0028 Evaluate side-chains 17 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9334 ------------------------------------------------------------------------------- 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: 10.0000 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 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: 0.7849 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8861 Z= 0.238 Angle : 0.733 9.334 12714 Z= 0.378 Chirality : 0.040 0.274 1498 Planarity : 0.006 0.073 1088 Dihedral : 23.951 179.650 2941 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 43.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 98.99 % 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: -2.17 (0.32), residues: 628 helix: -0.18 (0.31), residues: 273 sheet: -3.60 (0.77), residues: 34 loop : -2.38 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 82 HIS 0.008 0.002 HIS A 624 PHE 0.024 0.003 PHE A 67 TYR 0.018 0.002 TYR A 393 ARG 0.007 0.001 ARG A 674 ********************** 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 : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.3537 time to fit residues: 11.8529 Evaluate side-chains 19 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9206 ------------------------------------------------------------------------------- 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: 20.0000 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.041789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.033234 restraints weight = 139774.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.033932 restraints weight = 109639.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.034461 restraints weight = 91832.288| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8861 Z= 0.282 Angle : 0.784 9.564 12714 Z= 0.404 Chirality : 0.041 0.269 1498 Planarity : 0.007 0.072 1088 Dihedral : 24.018 179.521 2941 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 49.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 98.99 % 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: -2.34 (0.32), residues: 628 helix: -0.37 (0.31), residues: 272 sheet: -3.85 (0.76), residues: 35 loop : -2.39 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 82 HIS 0.005 0.002 HIS A 179 PHE 0.017 0.003 PHE A 67 TYR 0.018 0.002 TYR A 393 ARG 0.013 0.001 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.17 seconds wall clock time: 24 minutes 49.99 seconds (1489.99 seconds total)