Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 23:08:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/08_2023/8dvu_27745_updated.pdb" } resolution = 2.9 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 38 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3784 2.51 5 N 1059 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ASP 919": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5375 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 25, 'TRANS': 643} Chain breaks: 1 Chain: "B" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 766 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 36.881 19.714 31.150 1.00 7.69 S ATOM 4596 SG CYS A 813 34.935 16.553 31.282 1.00 10.45 S ATOM 4899 SG CYS A 864 36.768 16.868 27.740 1.00 13.54 S ATOM 4938 SG CYS A 869 33.961 19.186 29.142 1.00 16.27 S Time building chain proxies: 4.00, per 1000 atoms: 0.65 Number of scatterers: 6170 At special positions: 0 Unit cell: (94.218, 94.218, 71.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 38 15.00 Mg 1 11.99 O 1254 8.00 N 1059 7.00 C 3784 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: 2.78 Conformation dependent library (CDL) restraints added in 920.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " Number of angles added : 6 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 5 sheets defined 44.7% alpha, 8.2% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.673A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 446 through 451 removed outlier: 4.079A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 521 Processing helix chain 'A' and resid 528 through 557 removed outlier: 3.650A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.931A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.685A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 removed outlier: 3.791A pdb=" N SER A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 404 through 408 Processing sheet with id= B, first strand: chain 'A' and resid 457 through 462 Processing sheet with id= C, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.582A pdb=" N ILE A 693 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU A 661 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 695 " --> pdb=" O LEU A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 892 through 896 removed outlier: 5.935A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.277A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.80 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: 1358 1.33 - 1.45: 1471 1.45 - 1.57: 3416 1.57 - 1.69: 73 1.69 - 1.81: 46 Bond restraints: 6364 Sorted by residual: bond pdb=" C GLU A 716 " pdb=" O GLU A 716 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.30e-02 5.92e+03 2.59e+00 bond pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.26e+00 bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.69e-01 bond pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.46e-02 4.69e+03 7.81e-01 bond pdb=" CB PRO A 797 " pdb=" CG PRO A 797 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.35e-01 ... (remaining 6359 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.79: 425 107.79 - 114.89: 3858 114.89 - 121.99: 3212 121.99 - 129.09: 1209 129.09 - 136.19: 56 Bond angle restraints: 8760 Sorted by residual: angle pdb=" C GLY A 689 " pdb=" N ASP A 690 " pdb=" CA ASP A 690 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C GLU A 716 " pdb=" CA GLU A 716 " pdb=" CB GLU A 716 " ideal model delta sigma weight residual 111.86 108.41 3.45 1.34e+00 5.57e-01 6.62e+00 angle pdb=" N ALA A 440 " pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 110.64 114.09 -3.45 1.48e+00 4.57e-01 5.44e+00 angle pdb=" CA PRO A 797 " pdb=" C PRO A 797 " pdb=" O PRO A 797 " ideal model delta sigma weight residual 121.38 119.63 1.75 7.70e-01 1.69e+00 5.17e+00 angle pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " pdb=" CG1 VAL A 332 " ideal model delta sigma weight residual 110.40 114.15 -3.75 1.70e+00 3.46e-01 4.87e+00 ... (remaining 8755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3459 16.62 - 33.23: 238 33.23 - 49.85: 70 49.85 - 66.46: 16 66.46 - 83.08: 11 Dihedral angle restraints: 3794 sinusoidal: 1832 harmonic: 1962 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 7.39 -67.39 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N THR A 347 " pdb=" CA THR A 347 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 492 " pdb=" CB ASP A 492 " pdb=" CG ASP A 492 " pdb=" OD1 ASP A 492 " ideal model delta sinusoidal sigma weight residual -30.00 -87.59 57.59 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 683 0.032 - 0.064: 227 0.064 - 0.096: 64 0.096 - 0.128: 30 0.128 - 0.160: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA GLU A 716 " pdb=" N GLU A 716 " pdb=" C GLU A 716 " pdb=" CB GLU A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE A 439 " pdb=" CA ILE A 439 " pdb=" CG1 ILE A 439 " pdb=" CG2 ILE A 439 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1005 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 716 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU A 716 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A 716 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 717 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO A 382 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 8 " -0.009 2.00e-02 2.50e+03 6.30e-03 8.92e-01 pdb=" N1 U B 8 " 0.016 2.00e-02 2.50e+03 pdb=" C2 U B 8 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U B 8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 8 " 0.000 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 215 2.71 - 3.26: 5865 3.26 - 3.81: 10450 3.81 - 4.35: 13782 4.35 - 4.90: 21738 Nonbonded interactions: 52050 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O2B ADP A1003 " model vdw 2.164 2.170 nonbonded pdb=" O CYS A 829 " pdb=" O2' G B 10 " model vdw 2.250 2.440 nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.301 2.520 nonbonded pdb=" NZ LYS A 814 " pdb=" OE1 GLN A 902 " model vdw 2.308 2.520 nonbonded pdb=" NZ LYS A 458 " pdb=" OE2 GLU A 751 " model vdw 2.342 2.520 ... (remaining 52045 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: 0.380 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: 0.000 Extract box with map and model: 1.730 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 6364 Z= 0.145 Angle : 0.515 6.761 8760 Z= 0.290 Chirality : 0.038 0.160 1008 Planarity : 0.003 0.027 984 Dihedral : 13.391 83.078 2520 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 665 helix: -0.12 (0.27), residues: 316 sheet: -2.08 (0.47), residues: 92 loop : -2.99 (0.27), residues: 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.648 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 1.3047 time to fit residues: 155.3395 Evaluate side-chains 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.4518 time to fit residues: 2.2766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.0470 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 393 GLN A 517 GLN A 588 GLN A 708 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6364 Z= 0.206 Angle : 0.507 6.260 8760 Z= 0.256 Chirality : 0.040 0.156 1008 Planarity : 0.003 0.030 984 Dihedral : 5.606 73.294 1153 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 3.69 % 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: -1.29 (0.30), residues: 665 helix: 0.81 (0.28), residues: 319 sheet: -1.78 (0.47), residues: 89 loop : -2.71 (0.29), residues: 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.684 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 95 average time/residue: 1.2415 time to fit residues: 123.5962 Evaluate side-chains 88 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.6171 time to fit residues: 4.2317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 0.0570 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 6364 Z= 0.152 Angle : 0.478 6.067 8760 Z= 0.241 Chirality : 0.038 0.145 1008 Planarity : 0.003 0.031 984 Dihedral : 5.522 72.757 1153 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 3.69 % 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: -0.57 (0.31), residues: 665 helix: 1.37 (0.29), residues: 319 sheet: -1.31 (0.50), residues: 93 loop : -2.37 (0.31), residues: 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.702 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 1.2450 time to fit residues: 120.5105 Evaluate side-chains 88 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.5698 time to fit residues: 2.7583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 55 optimal weight: 0.0020 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6364 Z= 0.147 Angle : 0.478 6.533 8760 Z= 0.239 Chirality : 0.038 0.139 1008 Planarity : 0.003 0.031 984 Dihedral : 5.484 72.024 1153 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 3.69 % 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: -0.18 (0.32), residues: 665 helix: 1.73 (0.29), residues: 319 sheet: -1.17 (0.48), residues: 101 loop : -2.22 (0.32), residues: 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.676 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 94 average time/residue: 1.2047 time to fit residues: 119.0607 Evaluate side-chains 90 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.6824 time to fit residues: 4.6324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 6364 Z= 0.146 Angle : 0.476 7.564 8760 Z= 0.236 Chirality : 0.038 0.138 1008 Planarity : 0.003 0.031 984 Dihedral : 5.468 71.603 1153 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 3.52 % 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: 0.12 (0.32), residues: 665 helix: 2.00 (0.29), residues: 319 sheet: -1.00 (0.49), residues: 101 loop : -2.13 (0.33), residues: 245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.698 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 1.2230 time to fit residues: 114.4587 Evaluate side-chains 87 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1203 time to fit residues: 1.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 6364 Z= 0.321 Angle : 0.594 8.130 8760 Z= 0.296 Chirality : 0.043 0.180 1008 Planarity : 0.004 0.030 984 Dihedral : 6.183 91.413 1153 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 3.69 % 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: -0.18 (0.32), residues: 665 helix: 1.65 (0.29), residues: 319 sheet: -0.74 (0.53), residues: 79 loop : -2.23 (0.32), residues: 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.725 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 85 average time/residue: 1.3167 time to fit residues: 117.2319 Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1436 time to fit residues: 1.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.178 Angle : 0.517 8.466 8760 Z= 0.259 Chirality : 0.039 0.143 1008 Planarity : 0.003 0.032 984 Dihedral : 5.984 89.530 1153 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 2.51 % 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: 0.21 (0.32), residues: 665 helix: 1.91 (0.29), residues: 319 sheet: -0.62 (0.52), residues: 96 loop : -1.97 (0.34), residues: 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.844 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 1.2461 time to fit residues: 108.3985 Evaluate side-chains 85 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1203 time to fit residues: 1.1939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6364 Z= 0.205 Angle : 0.526 8.677 8760 Z= 0.263 Chirality : 0.040 0.154 1008 Planarity : 0.003 0.032 984 Dihedral : 6.003 91.115 1153 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.32), residues: 665 helix: 1.94 (0.29), residues: 319 sheet: -0.59 (0.52), residues: 96 loop : -1.93 (0.34), residues: 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.667 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 1.2950 time to fit residues: 109.2403 Evaluate side-chains 80 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0652 time to fit residues: 1.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN A 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6364 Z= 0.174 Angle : 0.509 8.685 8760 Z= 0.253 Chirality : 0.039 0.141 1008 Planarity : 0.003 0.033 984 Dihedral : 5.933 89.363 1153 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.32), residues: 665 helix: 2.05 (0.29), residues: 319 sheet: -0.57 (0.52), residues: 96 loop : -1.90 (0.34), residues: 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.655 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 1.2630 time to fit residues: 106.1961 Evaluate side-chains 80 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2168 time to fit residues: 1.1876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6364 Z= 0.191 Angle : 0.518 8.656 8760 Z= 0.258 Chirality : 0.039 0.150 1008 Planarity : 0.003 0.032 984 Dihedral : 5.955 89.970 1153 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 665 helix: 2.03 (0.29), residues: 319 sheet: -0.58 (0.52), residues: 96 loop : -1.89 (0.34), residues: 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.664 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 1.1821 time to fit residues: 99.6005 Evaluate side-chains 80 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1108 time to fit residues: 1.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.125093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104556 restraints weight = 6384.119| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.13 r_work: 0.2939 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 6364 Z= 0.231 Angle : 0.548 8.645 8760 Z= 0.275 Chirality : 0.040 0.148 1008 Planarity : 0.003 0.032 984 Dihedral : 6.121 94.907 1153 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 2.01 % 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: 0.24 (0.32), residues: 665 helix: 1.93 (0.29), residues: 319 sheet: -0.61 (0.54), residues: 84 loop : -1.90 (0.33), residues: 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.29 seconds wall clock time: 44 minutes 11.07 seconds (2651.07 seconds total)