Starting phenix.real_space_refine on Tue Feb 13 12:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/02_2024/8dvu_27745_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/02_2024/8dvu_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_27745/02_2024/8dvu_27745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/02_2024/8dvu_27745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/02_2024/8dvu_27745_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvu_27745/02_2024/8dvu_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.20, per 1000 atoms: 0.68 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: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.09 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: 2.47 Time building geometry restraints manager: 2.81 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: 3497 16.62 - 33.23: 250 33.23 - 49.85: 99 49.85 - 66.46: 59 66.46 - 83.08: 21 Dihedral angle restraints: 3926 sinusoidal: 1964 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 3923 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: 0.350 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: 1.550 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.520 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:16.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- 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 : 16.456 83.078 2652 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 % Allowed : 10.55 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 908 HIS 0.002 0.000 HIS A 876 PHE 0.008 0.001 PHE A 842 TYR 0.008 0.001 TYR A 390 ARG 0.001 0.000 ARG A 811 *********************** 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 : 0.695 Fit side-chains REVERT: A 369 MET cc_start: 0.9111 (mtm) cc_final: 0.8792 (mtm) REVERT: A 385 MET cc_start: 0.8671 (mmm) cc_final: 0.8470 (mmp) REVERT: A 492 ASP cc_start: 0.7216 (t70) cc_final: 0.6800 (t0) REVERT: A 498 GLN cc_start: 0.7766 (mm110) cc_final: 0.7544 (mp10) REVERT: A 560 MET cc_start: 0.8845 (mtt) cc_final: 0.8369 (mtt) REVERT: A 761 MET cc_start: 0.8748 (ttp) cc_final: 0.8516 (ttm) REVERT: A 786 HIS cc_start: 0.8184 (t70) cc_final: 0.7883 (t70) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 1.3748 time to fit residues: 163.5500 Evaluate side-chains 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 800 VAL 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: 3.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.4284 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6364 Z= 0.256 Angle : 0.543 6.417 8760 Z= 0.273 Chirality : 0.041 0.160 1008 Planarity : 0.003 0.030 984 Dihedral : 15.119 79.549 1292 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.69 % Allowed : 14.07 % Favored : 82.24 % 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: -1.35 (0.30), residues: 665 helix: 0.71 (0.28), residues: 319 sheet: -1.59 (0.49), residues: 79 loop : -2.73 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 771 HIS 0.003 0.001 HIS A 623 PHE 0.009 0.001 PHE A 842 TYR 0.015 0.002 TYR A 390 ARG 0.002 0.000 ARG A 502 *********************** 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 102 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.712 Fit side-chains REVERT: A 283 LYS cc_start: 0.8374 (mttp) cc_final: 0.8139 (mmtp) REVERT: A 369 MET cc_start: 0.9048 (mtm) cc_final: 0.8743 (mtm) REVERT: A 385 MET cc_start: 0.8672 (mmm) cc_final: 0.8407 (mmp) REVERT: A 479 MET cc_start: 0.9263 (mtp) cc_final: 0.8914 (mtp) REVERT: A 492 ASP cc_start: 0.7250 (t70) cc_final: 0.6845 (t0) REVERT: A 498 GLN cc_start: 0.7834 (mm110) cc_final: 0.7587 (mp10) REVERT: A 560 MET cc_start: 0.8914 (mtt) cc_final: 0.8435 (mtt) REVERT: A 679 LYS cc_start: 0.8413 (tttt) cc_final: 0.7937 (mtmm) REVERT: A 761 MET cc_start: 0.9001 (ttp) cc_final: 0.8725 (ttm) REVERT: A 786 HIS cc_start: 0.8249 (t70) cc_final: 0.7960 (t70) REVERT: A 906 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 914 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 919 ASP cc_start: 0.7076 (t0) cc_final: 0.6867 (t0) outliers start: 22 outliers final: 9 residues processed: 91 average time/residue: 1.3100 time to fit residues: 125.0703 Evaluate side-chains 85 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- 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: 0.8197 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6364 Z= 0.295 Angle : 0.576 6.214 8760 Z= 0.290 Chirality : 0.042 0.157 1008 Planarity : 0.004 0.033 984 Dihedral : 15.261 97.683 1291 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.02 % Allowed : 15.08 % Favored : 80.90 % 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: -0.91 (0.30), residues: 665 helix: 1.02 (0.29), residues: 319 sheet: -1.37 (0.48), residues: 89 loop : -2.46 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 908 HIS 0.004 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.017 0.002 TYR A 717 ARG 0.004 0.001 ARG A 533 *********************** 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 97 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.797 Fit side-chains REVERT: A 283 LYS cc_start: 0.8384 (mttp) cc_final: 0.8144 (mmtp) REVERT: A 312 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7584 (mtmm) REVERT: A 369 MET cc_start: 0.9004 (mtm) cc_final: 0.8702 (mtm) REVERT: A 385 MET cc_start: 0.8623 (mmm) cc_final: 0.8420 (mmp) REVERT: A 492 ASP cc_start: 0.7344 (t70) cc_final: 0.6896 (t0) REVERT: A 498 GLN cc_start: 0.7704 (mm110) cc_final: 0.7467 (mp10) REVERT: A 560 MET cc_start: 0.8945 (mtt) cc_final: 0.8438 (mtt) REVERT: A 679 LYS cc_start: 0.8435 (tttt) cc_final: 0.7933 (mttp) REVERT: A 761 MET cc_start: 0.9037 (ttp) cc_final: 0.8697 (ttm) REVERT: A 786 HIS cc_start: 0.8248 (t70) cc_final: 0.7968 (t70) REVERT: A 914 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6899 (tm-30) outliers start: 24 outliers final: 8 residues processed: 87 average time/residue: 1.2295 time to fit residues: 112.4900 Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6364 Z= 0.233 Angle : 0.538 7.223 8760 Z= 0.270 Chirality : 0.041 0.141 1008 Planarity : 0.003 0.034 984 Dihedral : 15.250 97.809 1291 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.35 % Allowed : 15.75 % Favored : 80.90 % 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: -0.53 (0.31), residues: 665 helix: 1.36 (0.29), residues: 319 sheet: -1.15 (0.49), residues: 89 loop : -2.33 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.016 0.002 TYR A 717 ARG 0.002 0.000 ARG A 533 *********************** 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 93 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.700 Fit side-chains REVERT: A 283 LYS cc_start: 0.8366 (mttp) cc_final: 0.8146 (mmtp) REVERT: A 479 MET cc_start: 0.9250 (mtp) cc_final: 0.8953 (mtp) REVERT: A 492 ASP cc_start: 0.7336 (t70) cc_final: 0.6872 (t0) REVERT: A 498 GLN cc_start: 0.7700 (mm110) cc_final: 0.7443 (mp10) REVERT: A 560 MET cc_start: 0.8949 (mtt) cc_final: 0.8450 (mtt) REVERT: A 679 LYS cc_start: 0.8447 (tttt) cc_final: 0.7959 (mttp) REVERT: A 761 MET cc_start: 0.9027 (ttp) cc_final: 0.8684 (ttm) REVERT: A 786 HIS cc_start: 0.8257 (t70) cc_final: 0.7994 (t70) REVERT: A 914 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6812 (tm-30) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 1.1761 time to fit residues: 103.9908 Evaluate side-chains 83 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.0470 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.1742 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= 0.210 Angle : 0.523 7.817 8760 Z= 0.262 Chirality : 0.040 0.138 1008 Planarity : 0.003 0.034 984 Dihedral : 15.252 97.323 1291 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.52 % Allowed : 16.92 % Favored : 79.56 % 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: -0.20 (0.32), residues: 665 helix: 1.58 (0.29), residues: 319 sheet: -0.85 (0.53), residues: 84 loop : -2.13 (0.32), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.018 0.002 TYR A 717 ARG 0.002 0.000 ARG A 533 *********************** 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 91 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.749 Fit side-chains REVERT: A 283 LYS cc_start: 0.8362 (mttp) cc_final: 0.8144 (mmtp) REVERT: A 479 MET cc_start: 0.9253 (mtp) cc_final: 0.8929 (mtp) REVERT: A 492 ASP cc_start: 0.7288 (t70) cc_final: 0.6822 (t0) REVERT: A 560 MET cc_start: 0.8957 (mtt) cc_final: 0.8476 (mtt) REVERT: A 679 LYS cc_start: 0.8458 (tttt) cc_final: 0.7963 (mttp) REVERT: A 741 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8505 (tp) REVERT: A 761 MET cc_start: 0.9018 (ttp) cc_final: 0.8667 (ttm) REVERT: A 786 HIS cc_start: 0.8261 (t70) cc_final: 0.7976 (t70) REVERT: A 914 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6911 (tm-30) outliers start: 21 outliers final: 10 residues processed: 85 average time/residue: 1.1997 time to fit residues: 107.3767 Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 0.0370 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.1645 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= 0.143 Angle : 0.480 8.263 8760 Z= 0.240 Chirality : 0.038 0.140 1008 Planarity : 0.003 0.035 984 Dihedral : 15.136 88.905 1288 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.18 % Allowed : 17.25 % Favored : 79.56 % 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: 0.22 (0.32), residues: 665 helix: 1.95 (0.29), residues: 319 sheet: -0.69 (0.52), residues: 96 loop : -1.99 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.002 0.001 HIS A 876 PHE 0.009 0.001 PHE A 842 TYR 0.017 0.001 TYR A 717 ARG 0.003 0.000 ARG A 734 *********************** 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 99 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.695 Fit side-chains REVERT: A 283 LYS cc_start: 0.8332 (mttp) cc_final: 0.8112 (mmtp) REVERT: A 479 MET cc_start: 0.9273 (mtp) cc_final: 0.8927 (mtp) REVERT: A 492 ASP cc_start: 0.7175 (t70) cc_final: 0.6696 (t0) REVERT: A 560 MET cc_start: 0.8955 (mtt) cc_final: 0.8501 (mtt) REVERT: A 679 LYS cc_start: 0.8464 (tttt) cc_final: 0.7980 (mttp) REVERT: A 761 MET cc_start: 0.8977 (ttp) cc_final: 0.8701 (ttm) REVERT: A 786 HIS cc_start: 0.8261 (t70) cc_final: 0.7982 (t70) REVERT: A 914 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: A 919 ASP cc_start: 0.7201 (t0) cc_final: 0.7001 (t0) outliers start: 19 outliers final: 9 residues processed: 92 average time/residue: 1.1438 time to fit residues: 110.6888 Evaluate side-chains 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU 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: 5.9990 chunk 56 optimal weight: 0.0020 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: 2.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6364 Z= 0.237 Angle : 0.549 8.907 8760 Z= 0.271 Chirality : 0.041 0.235 1008 Planarity : 0.003 0.033 984 Dihedral : 15.192 95.192 1288 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.02 % Allowed : 17.59 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.32), residues: 665 helix: 1.85 (0.29), residues: 319 sheet: -0.71 (0.53), residues: 84 loop : -1.92 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.003 0.001 HIS A 317 PHE 0.010 0.001 PHE A 842 TYR 0.019 0.002 TYR A 717 ARG 0.003 0.000 ARG A 734 *********************** 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 86 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.706 Fit side-chains REVERT: A 283 LYS cc_start: 0.8360 (mttp) cc_final: 0.8146 (mmtp) REVERT: A 492 ASP cc_start: 0.7197 (t70) cc_final: 0.6716 (t0) REVERT: A 560 MET cc_start: 0.8975 (mtt) cc_final: 0.8491 (mtt) REVERT: A 679 LYS cc_start: 0.8472 (tttt) cc_final: 0.7993 (mttp) REVERT: A 761 MET cc_start: 0.9032 (ttp) cc_final: 0.8693 (ttm) REVERT: A 786 HIS cc_start: 0.8275 (t70) cc_final: 0.7993 (t70) REVERT: A 914 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6919 (tm-30) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 1.2218 time to fit residues: 105.4762 Evaluate side-chains 81 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.8123 moved from start: 0.1722 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= 0.140 Angle : 0.497 9.152 8760 Z= 0.245 Chirality : 0.039 0.231 1008 Planarity : 0.003 0.034 984 Dihedral : 15.126 88.502 1288 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.51 % Allowed : 18.43 % Favored : 79.06 % 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: 0.45 (0.33), residues: 665 helix: 2.12 (0.29), residues: 319 sheet: -0.64 (0.52), residues: 96 loop : -1.82 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 771 HIS 0.002 0.000 HIS A 876 PHE 0.009 0.001 PHE A 842 TYR 0.014 0.001 TYR A 717 ARG 0.004 0.000 ARG A 734 *********************** 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 93 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.629 Fit side-chains REVERT: A 283 LYS cc_start: 0.8328 (mttp) cc_final: 0.8115 (mmtp) REVERT: A 492 ASP cc_start: 0.7173 (t70) cc_final: 0.6678 (t0) REVERT: A 498 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7336 (mp10) REVERT: A 560 MET cc_start: 0.8958 (mtt) cc_final: 0.8479 (mtt) REVERT: A 679 LYS cc_start: 0.8470 (tttt) cc_final: 0.7980 (mttp) REVERT: A 741 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 761 MET cc_start: 0.8965 (ttp) cc_final: 0.8572 (ttm) REVERT: A 786 HIS cc_start: 0.8270 (t70) cc_final: 0.7990 (t70) REVERT: A 914 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6807 (tm-30) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 1.2339 time to fit residues: 114.1538 Evaluate side-chains 88 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU 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: 0.4980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8134 moved from start: 0.1747 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= 0.163 Angle : 0.506 9.137 8760 Z= 0.250 Chirality : 0.039 0.230 1008 Planarity : 0.003 0.034 984 Dihedral : 15.115 87.032 1288 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.18 % Allowed : 18.93 % Favored : 78.89 % 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: 0.49 (0.32), residues: 665 helix: 2.17 (0.29), residues: 319 sheet: -0.64 (0.52), residues: 96 loop : -1.81 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 771 HIS 0.002 0.001 HIS A 623 PHE 0.009 0.001 PHE A 842 TYR 0.016 0.001 TYR A 717 ARG 0.003 0.000 ARG A 734 *********************** 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 85 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.655 Fit side-chains REVERT: A 283 LYS cc_start: 0.8328 (mttp) cc_final: 0.8119 (mmtp) REVERT: A 479 MET cc_start: 0.9210 (mtp) cc_final: 0.8908 (mtp) REVERT: A 492 ASP cc_start: 0.7156 (t70) cc_final: 0.6669 (t0) REVERT: A 498 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7337 (mp10) REVERT: A 560 MET cc_start: 0.8957 (mtt) cc_final: 0.8496 (mtt) REVERT: A 679 LYS cc_start: 0.8476 (tttt) cc_final: 0.7985 (mttp) REVERT: A 761 MET cc_start: 0.8993 (ttp) cc_final: 0.8576 (ttm) REVERT: A 786 HIS cc_start: 0.8278 (t70) cc_final: 0.7994 (t70) REVERT: A 914 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6821 (tm-30) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 1.2271 time to fit residues: 104.6029 Evaluate side-chains 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU 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: 0.6980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8162 moved from start: 0.1834 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= 0.204 Angle : 0.534 9.196 8760 Z= 0.264 Chirality : 0.040 0.233 1008 Planarity : 0.003 0.033 984 Dihedral : 15.151 90.814 1288 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.18 % Allowed : 19.10 % Favored : 78.73 % 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: 0.40 (0.32), residues: 665 helix: 2.07 (0.29), residues: 319 sheet: -0.69 (0.51), residues: 96 loop : -1.82 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.019 0.002 TYR A 717 ARG 0.003 0.000 ARG A 734 ********************** 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 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.717 Fit side-chains REVERT: A 283 LYS cc_start: 0.8346 (mttp) cc_final: 0.8136 (mmtp) REVERT: A 479 MET cc_start: 0.9216 (mtp) cc_final: 0.8923 (mtp) REVERT: A 492 ASP cc_start: 0.7193 (t70) cc_final: 0.6701 (t0) REVERT: A 498 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7357 (mp10) REVERT: A 560 MET cc_start: 0.8955 (mtt) cc_final: 0.8474 (mtt) REVERT: A 761 MET cc_start: 0.9022 (ttp) cc_final: 0.8658 (ttm) REVERT: A 786 HIS cc_start: 0.8280 (t70) cc_final: 0.7996 (t70) REVERT: A 914 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6827 (tm-30) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 1.2380 time to fit residues: 104.1658 Evaluate side-chains 84 residues out of total 597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.124569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.104109 restraints weight = 6386.558| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.13 r_work: 0.2962 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1833 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= 0.197 Angle : 0.533 9.321 8760 Z= 0.263 Chirality : 0.040 0.229 1008 Planarity : 0.003 0.033 984 Dihedral : 15.150 91.158 1288 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.51 % Allowed : 18.76 % Favored : 78.73 % 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: 0.41 (0.32), residues: 665 helix: 2.08 (0.29), residues: 319 sheet: -0.68 (0.51), residues: 96 loop : -1.80 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.022 0.002 TYR A 717 ARG 0.003 0.000 ARG A 734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.33 seconds wall clock time: 45 minutes 37.09 seconds (2737.09 seconds total)