Starting phenix.real_space_refine on Tue Feb 13 16:51:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3q_35154/02_2024/8i3q_35154.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3q_35154/02_2024/8i3q_35154.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/8i3q_35154/02_2024/8i3q_35154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3q_35154/02_2024/8i3q_35154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3q_35154/02_2024/8i3q_35154.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3q_35154/02_2024/8i3q_35154.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= 0.002 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 95 5.49 5 S 12 5.16 5 C 4057 2.51 5 N 1312 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 617": "OD1" <-> "OD2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6998 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2026 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 44, 'rna3p_pyr': 39} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain breaks: 1 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4971 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 556} Chain breaks: 4 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 6549 SG CYS A 711 29.245 14.332 41.891 1.00 82.48 S ATOM 6569 SG CYS A 714 27.687 10.896 43.793 1.00 85.07 S ATOM 6757 SG CYS A 735 31.613 10.871 41.848 1.00 98.72 S ATOM 6776 SG CYS A 738 28.630 10.360 40.525 1.00 97.60 S Time building chain proxies: 4.67, per 1000 atoms: 0.67 Number of scatterers: 6998 At special positions: 0 Unit cell: (85.68, 91.56, 99.96, 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 12 16.00 P 95 15.00 O 1521 8.00 N 1312 7.00 C 4057 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: 3.52 Conformation dependent library (CDL) restraints added in 955.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 738 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 711 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 735 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 714 " Number of angles added : 6 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 50.6% alpha, 8.2% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 35 through 65 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 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.636A pdb=" N SER A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.258A pdb=" N ASP A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 200 removed outlier: 4.619A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.153A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.526A pdb=" N GLU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.803A pdb=" N LEU A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.523A pdb=" N LYS A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 595 removed outlier: 3.515A pdb=" N HIS A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 647 removed outlier: 3.851A pdb=" N ASN A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.533A pdb=" N ASP A 669 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.604A pdb=" N ARG A 674 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.521A pdb=" N ILE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.998A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.723A pdb=" N TRP A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.819A pdb=" N ARG A 453 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 439 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 451 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 441 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 449 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE A 443 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 402 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511 removed outlier: 6.867A pdb=" N LEU A 510 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 700 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 654 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 524 removed outlier: 4.032A pdb=" N GLN A 531 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.505A pdb=" N VAL A 538 " --> pdb=" O TYR A 544 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1385 1.33 - 1.45: 2200 1.45 - 1.57: 3566 1.57 - 1.69: 188 1.69 - 1.81: 17 Bond restraints: 7356 Sorted by residual: bond pdb=" N LYS A 73 " pdb=" CA LYS A 73 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.51e+01 bond pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 1.525 1.485 0.040 1.32e-02 5.74e+03 9.11e+00 bond pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.06e-02 8.90e+03 9.11e+00 bond pdb=" N VAL A 710 " pdb=" CA VAL A 710 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.06e+00 bond pdb=" N ARG A 382 " pdb=" CA ARG A 382 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 8.01e+00 ... (remaining 7351 not shown) Histogram of bond angle deviations from ideal: 99.72 - 107.23: 786 107.23 - 114.74: 4306 114.74 - 122.25: 4038 122.25 - 129.76: 1156 129.76 - 137.27: 90 Bond angle restraints: 10376 Sorted by residual: angle pdb=" N ALA A 482 " pdb=" CA ALA A 482 " pdb=" C ALA A 482 " ideal model delta sigma weight residual 113.23 104.26 8.97 1.24e+00 6.50e-01 5.23e+01 angle pdb=" N LEU A 358 " pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 111.36 104.29 7.07 1.09e+00 8.42e-01 4.20e+01 angle pdb=" CA GLN A 483 " pdb=" CB GLN A 483 " pdb=" CG GLN A 483 " ideal model delta sigma weight residual 114.10 123.92 -9.82 2.00e+00 2.50e-01 2.41e+01 angle pdb=" C PHE A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.84 114.25 5.59 1.25e+00 6.40e-01 2.00e+01 angle pdb=" C ARG A 47 " pdb=" N LYS A 48 " pdb=" CA LYS A 48 " ideal model delta sigma weight residual 120.44 126.05 -5.61 1.30e+00 5.92e-01 1.86e+01 ... (remaining 10371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 4206 34.82 - 69.63: 349 69.63 - 104.45: 45 104.45 - 139.27: 5 139.27 - 174.08: 5 Dihedral angle restraints: 4610 sinusoidal: 2866 harmonic: 1744 Sorted by residual: dihedral pdb=" CD ARG A 382 " pdb=" NE ARG A 382 " pdb=" CZ ARG A 382 " pdb=" NH1 ARG A 382 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" O4' C C 38 " pdb=" C1' C C 38 " pdb=" N1 C C 38 " pdb=" C2 C C 38 " ideal model delta sinusoidal sigma weight residual -160.00 9.75 -169.75 1 1.50e+01 4.44e-03 8.47e+01 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 48.63 151.37 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1030 0.068 - 0.135: 103 0.135 - 0.203: 27 0.203 - 0.270: 4 0.270 - 0.338: 3 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA PHE A 398 " pdb=" N PHE A 398 " pdb=" C PHE A 398 " pdb=" CB PHE A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ASN A 42 " pdb=" N ASN A 42 " pdb=" C ASN A 42 " pdb=" CB ASN A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA CYS A 714 " pdb=" N CYS A 714 " pdb=" C CYS A 714 " pdb=" CB CYS A 714 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1164 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 382 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 382 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 382 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 382 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 382 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 462 " -0.328 9.50e-02 1.11e+02 1.47e-01 1.32e+01 pdb=" NE ARG A 462 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 462 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 462 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 462 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 714 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C CYS A 714 " 0.049 2.00e-02 2.50e+03 pdb=" O CYS A 714 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 715 " -0.017 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 17 2.39 - 3.02: 3754 3.02 - 3.64: 11191 3.64 - 4.27: 16937 4.27 - 4.90: 25742 Nonbonded interactions: 57641 Sorted by model distance: nonbonded pdb=" NE2 GLN A 723 " pdb=" NZ LYS A 734 " model vdw 1.762 3.200 nonbonded pdb=" O2' G C 74 " pdb=" O5' A C 75 " model vdw 2.169 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" OH TYR A 155 " model vdw 2.263 2.520 nonbonded pdb=" NH1 ARG A 754 " pdb=" OE1 GLU A 759 " model vdw 2.276 2.520 nonbonded pdb=" O2' A C 76 " pdb=" OP1 G C 77 " model vdw 2.279 2.440 ... (remaining 57636 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: 0.860 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: 3.170 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.170 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.005 0.049 7356 Z= 0.312 Angle : 0.829 12.269 10376 Z= 0.510 Chirality : 0.049 0.338 1167 Planarity : 0.017 0.493 1002 Dihedral : 22.354 174.081 3470 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.39 % Allowed : 4.43 % Favored : 90.17 % 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: 0.08 (0.34), residues: 585 helix: 1.56 (0.31), residues: 267 sheet: -0.12 (0.62), residues: 70 loop : -1.64 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 632 HIS 0.004 0.001 HIS A 681 PHE 0.016 0.002 PHE A 398 TYR 0.013 0.002 TYR A 18 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 0.681 Fit side-chains REVERT: A 570 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6653 (mtp-110) outliers start: 28 outliers final: 10 residues processed: 105 average time/residue: 0.4104 time to fit residues: 49.9381 Evaluate side-chains 44 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 485 GLN A 578 GLN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7356 Z= 0.170 Angle : 0.601 7.317 10376 Z= 0.307 Chirality : 0.037 0.211 1167 Planarity : 0.005 0.063 1002 Dihedral : 22.530 179.547 2169 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 8.67 % Favored : 88.44 % 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: 0.78 (0.35), residues: 585 helix: 2.34 (0.31), residues: 263 sheet: -0.14 (0.62), residues: 67 loop : -1.32 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.016 0.002 PHE A 81 TYR 0.015 0.001 TYR A 665 ARG 0.006 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.616 Fit side-chains REVERT: A 568 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8608 (tt) outliers start: 15 outliers final: 4 residues processed: 48 average time/residue: 0.2867 time to fit residues: 17.4007 Evaluate side-chains 27 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 46 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7356 Z= 0.156 Angle : 0.563 7.396 10376 Z= 0.287 Chirality : 0.036 0.192 1167 Planarity : 0.004 0.062 1002 Dihedral : 22.082 173.175 2151 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.16 % Allowed : 13.29 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.36), residues: 585 helix: 2.56 (0.31), residues: 265 sheet: -0.42 (0.61), residues: 72 loop : -1.01 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 632 HIS 0.002 0.001 HIS A 159 PHE 0.013 0.002 PHE A 50 TYR 0.010 0.001 TYR A 665 ARG 0.005 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.721 Fit side-chains REVERT: A 568 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8468 (tt) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.3610 time to fit residues: 16.1051 Evaluate side-chains 26 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7356 Z= 0.175 Angle : 0.569 7.494 10376 Z= 0.290 Chirality : 0.036 0.199 1167 Planarity : 0.005 0.066 1002 Dihedral : 22.067 172.148 2148 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.54 % Allowed : 15.80 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.36), residues: 585 helix: 2.72 (0.30), residues: 258 sheet: -0.43 (0.61), residues: 72 loop : -0.81 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.014 0.002 PHE A 50 TYR 0.009 0.001 TYR A 359 ARG 0.003 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.689 Fit side-chains REVERT: A 568 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8506 (tt) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.3423 time to fit residues: 15.5490 Evaluate side-chains 32 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7356 Z= 0.135 Angle : 0.530 7.536 10376 Z= 0.267 Chirality : 0.034 0.184 1167 Planarity : 0.004 0.064 1002 Dihedral : 21.969 171.573 2148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.35 % Allowed : 16.76 % Favored : 81.89 % 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 (0.36), residues: 585 helix: 2.87 (0.31), residues: 261 sheet: -0.07 (0.65), residues: 68 loop : -0.74 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 632 HIS 0.002 0.001 HIS A 159 PHE 0.010 0.001 PHE A 50 TYR 0.009 0.001 TYR A 359 ARG 0.002 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.667 Fit side-chains REVERT: A 568 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8471 (tt) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.3712 time to fit residues: 16.0293 Evaluate side-chains 31 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7356 Z= 0.176 Angle : 0.555 7.534 10376 Z= 0.282 Chirality : 0.035 0.198 1167 Planarity : 0.004 0.071 1002 Dihedral : 22.001 173.703 2148 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.54 % Allowed : 16.57 % Favored : 81.89 % 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: 1.39 (0.36), residues: 585 helix: 2.76 (0.30), residues: 260 sheet: -0.20 (0.62), residues: 72 loop : -0.73 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.014 0.002 PHE A 50 TYR 0.009 0.001 TYR A 359 ARG 0.004 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.717 Fit side-chains REVERT: A 568 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8485 (tt) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.3115 time to fit residues: 13.3101 Evaluate side-chains 31 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 65 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.0010 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7356 Z= 0.131 Angle : 0.524 7.555 10376 Z= 0.264 Chirality : 0.034 0.185 1167 Planarity : 0.004 0.072 1002 Dihedral : 21.943 173.495 2148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.73 % Allowed : 16.38 % Favored : 81.89 % 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: 1.59 (0.36), residues: 585 helix: 2.95 (0.30), residues: 260 sheet: -0.04 (0.60), residues: 77 loop : -0.69 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 632 HIS 0.002 0.001 HIS A 159 PHE 0.009 0.001 PHE A 50 TYR 0.010 0.001 TYR A 359 ARG 0.003 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.737 Fit side-chains REVERT: A 568 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8496 (tt) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.3653 time to fit residues: 15.4968 Evaluate side-chains 31 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7356 Z= 0.259 Angle : 0.620 7.555 10376 Z= 0.316 Chirality : 0.038 0.210 1167 Planarity : 0.005 0.072 1002 Dihedral : 22.107 176.294 2148 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.73 % Allowed : 17.15 % Favored : 81.12 % 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: 1.11 (0.35), residues: 585 helix: 2.53 (0.30), residues: 258 sheet: -0.32 (0.60), residues: 78 loop : -0.89 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.017 0.002 PHE A 50 TYR 0.010 0.002 TYR A 359 ARG 0.004 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.739 Fit side-chains REVERT: A 568 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8597 (tt) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 0.2966 time to fit residues: 13.1400 Evaluate side-chains 30 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7356 Z= 0.152 Angle : 0.550 7.578 10376 Z= 0.279 Chirality : 0.035 0.191 1167 Planarity : 0.005 0.081 1002 Dihedral : 22.025 175.018 2148 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.16 % Allowed : 17.15 % Favored : 81.70 % 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: 1.31 (0.36), residues: 585 helix: 2.75 (0.30), residues: 259 sheet: -0.58 (0.59), residues: 83 loop : -0.70 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.011 0.001 PHE A 50 TYR 0.011 0.001 TYR A 359 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.723 Fit side-chains REVERT: A 485 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6983 (mm110) REVERT: A 568 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 577 LEU cc_start: 0.8277 (mt) cc_final: 0.8075 (mt) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.3240 time to fit residues: 13.2737 Evaluate side-chains 29 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7356 Z= 0.153 Angle : 0.547 7.556 10376 Z= 0.276 Chirality : 0.035 0.191 1167 Planarity : 0.004 0.078 1002 Dihedral : 21.995 174.924 2148 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.16 % Allowed : 16.96 % Favored : 81.89 % 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: 1.45 (0.36), residues: 585 helix: 2.86 (0.30), residues: 259 sheet: -0.08 (0.61), residues: 77 loop : -0.80 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.012 0.001 PHE A 50 TYR 0.011 0.001 TYR A 359 ARG 0.002 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.684 Fit side-chains REVERT: A 568 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 577 LEU cc_start: 0.8250 (mt) cc_final: 0.8033 (mt) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.3408 time to fit residues: 12.5904 Evaluate side-chains 29 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0470 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.137945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.105898 restraints weight = 12066.486| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.92 r_work: 0.3382 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7356 Z= 0.163 Angle : 0.554 7.547 10376 Z= 0.281 Chirality : 0.035 0.196 1167 Planarity : 0.005 0.074 1002 Dihedral : 22.014 175.608 2148 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.16 % Allowed : 16.96 % Favored : 81.89 % 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: 1.44 (0.36), residues: 585 helix: 2.91 (0.30), residues: 259 sheet: -0.19 (0.61), residues: 78 loop : -0.83 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 632 HIS 0.003 0.001 HIS A 159 PHE 0.013 0.001 PHE A 50 TYR 0.011 0.001 TYR A 359 ARG 0.003 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.57 seconds wall clock time: 30 minutes 56.43 seconds (1856.43 seconds total)