Starting phenix.real_space_refine on Fri Dec 8 06:01:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmf_22257/12_2023/6xmf_22257.pdb" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 109 5.49 5 S 11 5.16 5 C 4235 2.51 5 N 1381 2.21 5 O 1645 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 21": "OE1" <-> "OE2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" 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 GLU 666": "OE1" <-> "OE2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" 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: 7382 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5054 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 38, 'TRANS': 588} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2327 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 46} Link IDs: {'rna2p': 13, 'rna3p': 95} Chain breaks: 2 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 4607 SG CYS A 711 52.215 79.966 49.609 1.00 49.88 S ATOM 4627 SG CYS A 714 51.876 82.146 46.526 1.00 58.23 S ATOM 4815 SG CYS A 735 55.331 81.541 48.049 1.00 66.85 S ATOM 4834 SG CYS A 738 52.449 83.643 49.885 1.00 68.17 S Time building chain proxies: 4.56, per 1000 atoms: 0.62 Number of scatterers: 7382 At special positions: 0 Unit cell: (84, 93.45, 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 109 15.00 O 1645 8.00 N 1381 7.00 C 4235 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: 3.38 Conformation dependent library (CDL) restraints added in 896.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 711 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 738 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 735 " Number of angles added : 6 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 51.2% alpha, 5.9% beta 30 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.864A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 65 " --> pdb=" O CYS A 61 " (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: 3.756A pdb=" N PHE A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.758A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.642A pdb=" N SER A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 4.052A pdb=" N ASP A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.708A pdb=" N TRP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.812A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.873A pdb=" N LYS A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.781A pdb=" N LYS A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.810A pdb=" N ARG A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 5.001A 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 466 through 476 removed outlier: 3.562A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.593A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.745A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.729A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.506A pdb=" N GLU A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 647 removed outlier: 3.750A pdb=" N VAL A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 4.187A pdb=" N GLU A 666 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.552A pdb=" N PHE A 678 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.531A pdb=" N ILE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 3.909A pdb=" N ARG A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.829A 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 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 533 through 535 removed outlier: 3.850A pdb=" N PHE A 533 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 521 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 519 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 510 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 652 " --> pdb=" O VAL A 700 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 990 1.32 - 1.44: 2756 1.44 - 1.56: 3793 1.56 - 1.69: 215 1.69 - 1.81: 16 Bond restraints: 7770 Sorted by residual: bond pdb=" N ASP A 617 " pdb=" CA ASP A 617 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.16e-02 7.43e+03 1.29e+01 bond pdb=" C ASP A 617 " pdb=" O ASP A 617 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.16e-02 7.43e+03 1.20e+01 bond pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.61e-02 3.86e+03 7.18e+00 bond pdb=" CA LEU A 618 " pdb=" C LEU A 618 " ideal model delta sigma weight residual 1.526 1.538 -0.012 9.70e-03 1.06e+04 1.45e+00 bond pdb=" C3' G C 74 " pdb=" O3' G C 74 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.40e+00 ... (remaining 7765 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 800 106.76 - 113.56: 4240 113.56 - 120.37: 3039 120.37 - 127.18: 2654 127.18 - 133.99: 282 Bond angle restraints: 11015 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 103.00 110.38 -7.38 1.10e+00 8.26e-01 4.50e+01 angle pdb=" N ILE A 537 " pdb=" CA ILE A 537 " pdb=" C ILE A 537 " ideal model delta sigma weight residual 106.21 111.69 -5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" O ASP A 617 " pdb=" C ASP A 617 " pdb=" N LEU A 618 " ideal model delta sigma weight residual 122.08 117.60 4.48 1.07e+00 8.73e-01 1.75e+01 angle pdb=" CA LEU A 618 " pdb=" C LEU A 618 " pdb=" O LEU A 618 " ideal model delta sigma weight residual 121.86 116.85 5.01 1.39e+00 5.18e-01 1.30e+01 angle pdb=" C ASN A 239 " pdb=" N CYS A 240 " pdb=" CA CYS A 240 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.28e+01 ... (remaining 11010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 4460 35.82 - 71.64: 268 71.64 - 107.45: 48 107.45 - 143.27: 2 143.27 - 179.09: 5 Dihedral angle restraints: 4783 sinusoidal: 2951 harmonic: 1832 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 45.74 154.26 1 1.50e+01 4.44e-03 8.11e+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 -128.00 51.09 -179.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" N PRO A 534 " pdb=" CA PRO A 534 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1122 0.046 - 0.093: 116 0.093 - 0.139: 19 0.139 - 0.186: 7 0.186 - 0.232: 1 Chirality restraints: 1265 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 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 -2.30 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C3' G C 74 " pdb=" C4' G C 74 " pdb=" O3' G C 74 " pdb=" C2' G C 74 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 1262 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 618 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU A 618 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A 618 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 619 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 616 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C PHE A 616 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE A 616 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 617 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 428 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 429 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.029 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1442 2.78 - 3.31: 6748 3.31 - 3.84: 13218 3.84 - 4.37: 16387 4.37 - 4.90: 24309 Nonbonded interactions: 62104 Sorted by model distance: nonbonded pdb=" OH TYR A 377 " pdb=" O2' A C 41 " model vdw 2.246 2.440 nonbonded pdb=" O2' A C 76 " pdb=" OP1 G C 77 " model vdw 2.250 2.440 nonbonded pdb=" O PRO A 77 " pdb=" OG SER A 132 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 427 " pdb=" OP2 C C 112 " model vdw 2.319 2.440 nonbonded pdb=" O2' U C 13 " pdb=" OP2 G C 22 " model vdw 2.323 2.440 ... (remaining 62099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.010 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 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 0.043 7770 Z= 0.144 Angle : 0.562 7.375 11015 Z= 0.346 Chirality : 0.032 0.232 1265 Planarity : 0.004 0.051 1035 Dihedral : 20.609 179.092 3585 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.78 (0.33), residues: 615 helix: -0.64 (0.31), residues: 283 sheet: -0.98 (0.67), residues: 62 loop : -1.73 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.002 0.001 HIS A 200 PHE 0.006 0.001 PHE A 108 TYR 0.010 0.001 TYR A 377 ARG 0.018 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.649 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3166 time to fit residues: 26.2301 Evaluate side-chains 42 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 723 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7770 Z= 0.269 Angle : 0.649 7.812 11015 Z= 0.331 Chirality : 0.037 0.250 1265 Planarity : 0.005 0.050 1035 Dihedral : 21.684 178.276 2309 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 1.79 % Allowed : 7.74 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.33), residues: 615 helix: -0.14 (0.30), residues: 291 sheet: -1.47 (0.69), residues: 56 loop : -1.95 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 632 HIS 0.005 0.001 HIS A 576 PHE 0.016 0.002 PHE A 756 TYR 0.012 0.002 TYR A 175 ARG 0.006 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.644 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.2731 time to fit residues: 20.0084 Evaluate side-chains 50 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0697 time to fit residues: 1.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 40.0000 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS ** 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: 0.7194 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7770 Z= 0.428 Angle : 0.718 9.276 11015 Z= 0.368 Chirality : 0.041 0.248 1265 Planarity : 0.006 0.054 1035 Dihedral : 21.884 175.104 2309 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.38 % Allowed : 12.10 % Favored : 85.52 % 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: -1.66 (0.33), residues: 615 helix: -0.37 (0.29), residues: 291 sheet: -1.56 (0.69), residues: 59 loop : -1.76 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 82 HIS 0.007 0.002 HIS A 159 PHE 0.026 0.003 PHE A 420 TYR 0.020 0.002 TYR A 393 ARG 0.010 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.604 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.3104 time to fit residues: 20.8837 Evaluate side-chains 51 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0701 time to fit residues: 1.6299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7770 Z= 0.186 Angle : 0.570 6.995 11015 Z= 0.293 Chirality : 0.035 0.241 1265 Planarity : 0.004 0.053 1035 Dihedral : 21.756 179.746 2309 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.98 % Allowed : 13.89 % Favored : 84.13 % 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: -1.25 (0.34), residues: 615 helix: 0.14 (0.30), residues: 294 sheet: -1.89 (0.66), residues: 60 loop : -1.64 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 159 PHE 0.013 0.002 PHE A 108 TYR 0.015 0.002 TYR A 393 ARG 0.007 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.584 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.3071 time to fit residues: 21.4999 Evaluate side-chains 53 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0814 time to fit residues: 1.9679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7770 Z= 0.261 Angle : 0.592 7.718 11015 Z= 0.305 Chirality : 0.036 0.242 1265 Planarity : 0.005 0.052 1035 Dihedral : 21.689 177.716 2309 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 1.59 % Allowed : 15.08 % Favored : 83.33 % 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: -1.33 (0.34), residues: 615 helix: 0.09 (0.29), residues: 301 sheet: -1.77 (0.68), residues: 59 loop : -1.80 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 82 HIS 0.006 0.001 HIS A 159 PHE 0.018 0.002 PHE A 420 TYR 0.016 0.002 TYR A 393 ARG 0.011 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.625 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.3152 time to fit residues: 21.4625 Evaluate side-chains 47 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0755 time to fit residues: 1.6178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7770 Z= 0.238 Angle : 0.579 7.633 11015 Z= 0.298 Chirality : 0.035 0.242 1265 Planarity : 0.004 0.052 1035 Dihedral : 21.658 178.429 2309 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.79 % Allowed : 16.27 % Favored : 81.94 % 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: -1.26 (0.34), residues: 615 helix: 0.23 (0.30), residues: 300 sheet: -1.80 (0.68), residues: 60 loop : -1.85 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 82 HIS 0.006 0.001 HIS A 159 PHE 0.016 0.002 PHE A 420 TYR 0.016 0.002 TYR A 393 ARG 0.008 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.606 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.3095 time to fit residues: 20.1362 Evaluate side-chains 48 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0744 time to fit residues: 1.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7770 Z= 0.182 Angle : 0.563 7.851 11015 Z= 0.288 Chirality : 0.034 0.240 1265 Planarity : 0.004 0.052 1035 Dihedral : 21.586 179.222 2309 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 1.19 % Allowed : 16.67 % Favored : 82.14 % 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: -0.92 (0.34), residues: 615 helix: 0.48 (0.30), residues: 301 sheet: -1.62 (0.70), residues: 56 loop : -1.66 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.004 0.001 HIS A 159 PHE 0.014 0.002 PHE A 420 TYR 0.011 0.001 TYR A 175 ARG 0.011 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.719 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.3406 time to fit residues: 21.9531 Evaluate side-chains 45 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0657 time to fit residues: 1.1453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7770 Z= 0.220 Angle : 0.581 10.178 11015 Z= 0.296 Chirality : 0.035 0.240 1265 Planarity : 0.005 0.052 1035 Dihedral : 21.537 177.935 2309 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 1.19 % Allowed : 16.67 % Favored : 82.14 % 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: -0.90 (0.34), residues: 615 helix: 0.54 (0.30), residues: 302 sheet: -1.51 (0.71), residues: 56 loop : -1.75 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 159 PHE 0.015 0.002 PHE A 420 TYR 0.012 0.001 TYR A 175 ARG 0.012 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.671 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.3548 time to fit residues: 21.4499 Evaluate side-chains 47 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0799 time to fit residues: 1.4583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7770 Z= 0.212 Angle : 0.578 9.778 11015 Z= 0.294 Chirality : 0.035 0.240 1265 Planarity : 0.005 0.057 1035 Dihedral : 21.510 178.362 2309 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.40 % Allowed : 17.86 % Favored : 81.75 % 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: -0.77 (0.34), residues: 615 helix: 0.63 (0.30), residues: 300 sheet: -1.48 (0.70), residues: 56 loop : -1.63 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 159 PHE 0.015 0.002 PHE A 420 TYR 0.011 0.001 TYR A 175 ARG 0.013 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.669 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.3526 time to fit residues: 20.3035 Evaluate side-chains 42 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0697 time to fit residues: 0.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 0.035 7770 Z= 0.241 Angle : 0.592 10.573 11015 Z= 0.301 Chirality : 0.036 0.240 1265 Planarity : 0.005 0.059 1035 Dihedral : 21.496 177.716 2309 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 18.25 % Favored : 81.75 % 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: -0.81 (0.34), residues: 615 helix: 0.59 (0.30), residues: 300 sheet: -1.46 (0.71), residues: 56 loop : -1.66 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 82 HIS 0.005 0.001 HIS A 159 PHE 0.016 0.002 PHE A 420 TYR 0.012 0.001 TYR A 175 ARG 0.013 0.001 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.678 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.3699 time to fit residues: 20.0478 Evaluate side-chains 41 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.206156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154706 restraints weight = 7840.334| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.46 r_work: 0.3741 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7770 Z= 0.164 Angle : 0.560 10.651 11015 Z= 0.285 Chirality : 0.034 0.239 1265 Planarity : 0.004 0.059 1035 Dihedral : 21.441 179.135 2309 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.60 % Allowed : 17.86 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 615 helix: 1.04 (0.31), residues: 290 sheet: -1.51 (0.69), residues: 56 loop : -1.55 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.003 0.001 HIS A 159 PHE 0.013 0.002 PHE A 108 TYR 0.011 0.001 TYR A 175 ARG 0.014 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.59 seconds wall clock time: 30 minutes 12.00 seconds (1812.00 seconds total)