Starting phenix.real_space_refine on Tue Feb 13 12:13:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvs_27744/02_2024/8dvs_27744_updated.pdb" } resolution = 3.0 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= 0.012 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 27 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3756 2.51 5 N 1038 2.21 5 O 1202 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 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6058 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5479 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 653} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna3p': 25} 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 4555 SG CYS A 810 42.435 21.036 29.261 1.00 21.81 S ATOM 4994 SG CYS A 864 42.810 19.059 25.632 1.00 25.59 S ATOM 5033 SG CYS A 869 39.720 20.716 26.736 1.00 33.77 S Time building chain proxies: 4.17, per 1000 atoms: 0.69 Number of scatterers: 6058 At special positions: 0 Unit cell: (91.92, 95.367, 68.94, 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 27 15.00 Mg 1 11.99 O 1202 8.00 N 1038 7.00 C 3756 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: 2.64 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 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 6 sheets defined 44.0% alpha, 7.0% beta 12 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 334 through 339 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 434 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 470 through 489 removed outlier: 4.090A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 521 Processing helix chain 'A' and resid 530 through 557 removed outlier: 3.516A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 581 through 602 removed outlier: 3.943A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 removed outlier: 4.393A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 745 through 770 removed outlier: 4.075A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 Processing helix chain 'A' and resid 836 through 841 removed outlier: 4.065A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N CYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 836 through 841' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing sheet with id= A, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= B, first strand: chain 'A' and resid 460 through 462 removed outlier: 7.532A pdb=" N ARG A 461 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 740 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 902 through 904 removed outlier: 6.027A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 Processing sheet with id= F, first strand: chain 'A' and resid 874 through 878 214 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1858 1.34 - 1.46: 1000 1.46 - 1.57: 3277 1.57 - 1.69: 52 1.69 - 1.81: 46 Bond restraints: 6233 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.15e-01 bond pdb=" CA ILE A 884 " pdb=" C ILE A 884 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.05e-02 9.07e+03 7.09e-01 bond pdb=" CA ILE A 704 " pdb=" CB ILE A 704 " ideal model delta sigma weight residual 1.551 1.542 0.009 1.08e-02 8.57e+03 6.62e-01 bond pdb=" CA GLN A 794 " pdb=" CB GLN A 794 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.31e-02 5.83e+03 5.77e-01 bond pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.30e-02 5.92e+03 4.09e-01 ... (remaining 6228 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.75: 360 107.75 - 114.81: 3774 114.81 - 121.87: 3111 121.87 - 128.93: 1240 128.93 - 136.00: 52 Bond angle restraints: 8537 Sorted by residual: angle pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta sigma weight residual 120.49 124.17 -3.68 1.38e+00 5.25e-01 7.11e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.81 110.08 1.73 8.60e-01 1.35e+00 4.06e+00 angle pdb=" CA LEU A 653 " pdb=" CB LEU A 653 " pdb=" CG LEU A 653 " ideal model delta sigma weight residual 116.30 123.21 -6.91 3.50e+00 8.16e-02 3.90e+00 angle pdb=" CA GLY A 413 " pdb=" C GLY A 413 " pdb=" O GLY A 413 " ideal model delta sigma weight residual 122.39 120.61 1.78 9.30e-01 1.16e+00 3.68e+00 angle pdb=" O1B ADP A1003 " pdb=" PB ADP A1003 " pdb=" O2B ADP A1003 " ideal model delta sigma weight residual 119.90 114.15 5.75 3.00e+00 1.11e-01 3.67e+00 ... (remaining 8532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 3606 25.17 - 50.35: 165 50.35 - 75.52: 52 75.52 - 100.70: 6 100.70 - 125.87: 3 Dihedral angle restraints: 3832 sinusoidal: 1830 harmonic: 2002 Sorted by residual: dihedral pdb=" C5' ADP A1003 " pdb=" O5' ADP A1003 " pdb=" PA ADP A1003 " pdb=" O2A ADP A1003 " ideal model delta sinusoidal sigma weight residual 300.00 174.13 125.87 1 2.00e+01 2.50e-03 3.81e+01 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 47.56 -107.56 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" O1B ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PB ADP A1003 " pdb=" PA ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 46.73 -106.73 1 2.00e+01 2.50e-03 3.09e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 669 0.030 - 0.059: 197 0.059 - 0.089: 62 0.089 - 0.118: 40 0.118 - 0.148: 2 Chirality restraints: 970 Sorted by residual: chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 695 " pdb=" N ILE A 695 " pdb=" C ILE A 695 " pdb=" CB ILE A 695 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 967 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 382 " 0.047 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=" C ILE A 300 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 301 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 884 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 885 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 885 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 885 " -0.014 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1518 2.80 - 3.32: 5477 3.32 - 3.85: 10399 3.85 - 4.37: 12214 4.37 - 4.90: 20254 Nonbonded interactions: 49862 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.271 2.520 nonbonded pdb=" OD2 ASP A 701 " pdb=" OH TYR A 717 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 441 " pdb=" OE1 GLN A 769 " model vdw 2.316 2.440 nonbonded pdb=" O ASN A 625 " pdb=" OG1 THR A 628 " model vdw 2.324 2.440 nonbonded pdb=" OE1 GLN A 511 " pdb=" N2 G B 56 " model vdw 2.344 2.520 ... (remaining 49857 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.580 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.019 6233 Z= 0.103 Angle : 0.467 6.908 8537 Z= 0.259 Chirality : 0.036 0.148 970 Planarity : 0.003 0.027 997 Dihedral : 15.921 125.869 2532 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.32 % Allowed : 8.72 % Favored : 89.97 % 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: -1.94 (0.29), residues: 680 helix: 0.68 (0.27), residues: 300 sheet: -2.50 (0.44), residues: 112 loop : -3.08 (0.28), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 646 HIS 0.001 0.000 HIS A 375 PHE 0.007 0.001 PHE A 853 TYR 0.007 0.001 TYR A 246 ARG 0.001 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.672 Fit side-chains REVERT: A 425 ASP cc_start: 0.7298 (t0) cc_final: 0.6952 (t0) REVERT: A 510 GLU cc_start: 0.7944 (tt0) cc_final: 0.7741 (tt0) REVERT: A 593 LYS cc_start: 0.7826 (mttm) cc_final: 0.7467 (mtmm) REVERT: A 661 LEU cc_start: 0.8114 (tp) cc_final: 0.7885 (tp) REVERT: A 679 LYS cc_start: 0.7667 (tttt) cc_final: 0.6766 (tttt) REVERT: A 726 GLN cc_start: 0.7428 (mt0) cc_final: 0.7125 (mt0) REVERT: A 790 ILE cc_start: 0.8349 (mt) cc_final: 0.8092 (mp) REVERT: A 853 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6017 (p90) outliers start: 8 outliers final: 5 residues processed: 132 average time/residue: 1.3381 time to fit residues: 184.1731 Evaluate side-chains 88 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 305 GLN A 306 GLN A 336 GLN A 341 ASN A 381 HIS A 419 ASN A 451 GLN A 457 GLN A 495 ASN A 517 GLN A 524 GLN A 584 GLN A 619 GLN A 668 ASN A 678 GLN A 708 GLN A 769 GLN A 830 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6233 Z= 0.183 Angle : 0.534 11.196 8537 Z= 0.248 Chirality : 0.040 0.205 970 Planarity : 0.003 0.033 997 Dihedral : 14.068 100.826 1147 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.29 % Allowed : 15.95 % Favored : 80.76 % 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: -0.69 (0.31), residues: 680 helix: 1.64 (0.29), residues: 304 sheet: -2.15 (0.47), residues: 100 loop : -2.27 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 771 HIS 0.003 0.001 HIS A 830 PHE 0.019 0.002 PHE A 853 TYR 0.019 0.001 TYR A 566 ARG 0.002 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.696 Fit side-chains REVERT: A 425 ASP cc_start: 0.7340 (t0) cc_final: 0.7006 (t0) REVERT: A 447 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 498 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: A 503 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6923 (mt-10) REVERT: A 593 LYS cc_start: 0.7859 (mttm) cc_final: 0.7378 (mttp) REVERT: A 673 MET cc_start: 0.8442 (ptp) cc_final: 0.7960 (ptp) REVERT: A 679 LYS cc_start: 0.7685 (tttt) cc_final: 0.6845 (tttt) outliers start: 20 outliers final: 7 residues processed: 91 average time/residue: 1.2533 time to fit residues: 119.4110 Evaluate side-chains 74 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 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 457 GLN A 495 ASN A 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6233 Z= 0.194 Angle : 0.526 10.193 8537 Z= 0.249 Chirality : 0.040 0.181 970 Planarity : 0.003 0.037 997 Dihedral : 13.968 92.989 1143 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.10 % Allowed : 16.28 % Favored : 78.62 % 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: 680 helix: 1.99 (0.30), residues: 308 sheet: -1.97 (0.47), residues: 100 loop : -1.99 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 381 PHE 0.020 0.001 PHE A 853 TYR 0.015 0.001 TYR A 566 ARG 0.002 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.7555 (t0) cc_final: 0.7189 (t0) REVERT: A 479 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (mtm) REVERT: A 498 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: A 593 LYS cc_start: 0.7892 (mttm) cc_final: 0.7275 (mttp) REVERT: A 595 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: A 653 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7882 (pp) REVERT: A 679 LYS cc_start: 0.7613 (tttt) cc_final: 0.6768 (tttt) REVERT: A 730 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7383 (ttm-80) REVERT: A 882 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6708 (p90) outliers start: 31 outliers final: 12 residues processed: 90 average time/residue: 1.3030 time to fit residues: 122.7375 Evaluate side-chains 82 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 767 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 336 GLN A 451 GLN A 457 GLN A 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6233 Z= 0.198 Angle : 0.523 10.236 8537 Z= 0.248 Chirality : 0.039 0.163 970 Planarity : 0.003 0.036 997 Dihedral : 13.948 89.216 1143 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.44 % Allowed : 17.93 % Favored : 77.63 % 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: 0.00 (0.32), residues: 680 helix: 2.15 (0.29), residues: 308 sheet: -1.80 (0.48), residues: 100 loop : -1.89 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.006 0.001 HIS A 317 PHE 0.022 0.001 PHE A 853 TYR 0.015 0.001 TYR A 566 ARG 0.004 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.7546 (t0) cc_final: 0.7162 (t0) REVERT: A 479 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: A 498 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 593 LYS cc_start: 0.7925 (mttm) cc_final: 0.7303 (mttp) REVERT: A 595 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: A 629 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7964 (pt) REVERT: A 653 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7859 (pp) REVERT: A 679 LYS cc_start: 0.7841 (tttt) cc_final: 0.7035 (tttt) REVERT: A 724 MET cc_start: 0.8622 (ttp) cc_final: 0.8381 (ttp) REVERT: A 730 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7440 (ttm-80) REVERT: A 787 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 882 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6787 (p90) outliers start: 27 outliers final: 13 residues processed: 84 average time/residue: 1.2091 time to fit residues: 106.8510 Evaluate side-chains 85 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6233 Z= 0.149 Angle : 0.495 9.251 8537 Z= 0.233 Chirality : 0.038 0.150 970 Planarity : 0.003 0.036 997 Dihedral : 13.889 84.436 1143 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.44 % Allowed : 18.75 % Favored : 76.81 % 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: 0.23 (0.32), residues: 680 helix: 2.35 (0.29), residues: 307 sheet: -1.75 (0.47), residues: 100 loop : -1.74 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 PHE 0.018 0.001 PHE A 853 TYR 0.014 0.001 TYR A 566 ARG 0.004 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.669 Fit side-chains REVERT: A 425 ASP cc_start: 0.7521 (t0) cc_final: 0.7154 (t0) REVERT: A 498 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: A 503 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 591 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 593 LYS cc_start: 0.7997 (mttm) cc_final: 0.7353 (mttp) REVERT: A 595 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: A 653 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 664 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6422 (mmp80) REVERT: A 679 LYS cc_start: 0.7845 (tttt) cc_final: 0.7082 (tttm) REVERT: A 730 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6937 (ttm-80) REVERT: A 853 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6358 (p90) REVERT: A 882 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6783 (p90) outliers start: 27 outliers final: 12 residues processed: 82 average time/residue: 1.2888 time to fit residues: 110.8683 Evaluate side-chains 83 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6233 Z= 0.178 Angle : 0.514 9.468 8537 Z= 0.246 Chirality : 0.039 0.142 970 Planarity : 0.003 0.036 997 Dihedral : 13.909 88.459 1143 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.61 % Allowed : 19.41 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.32), residues: 680 helix: 2.42 (0.29), residues: 307 sheet: -1.73 (0.46), residues: 100 loop : -1.68 (0.34), residues: 273 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 0.020 0.001 PHE A 853 TYR 0.014 0.001 TYR A 566 ARG 0.004 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 64 time to evaluate : 0.723 Fit side-chains REVERT: A 498 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: A 503 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 593 LYS cc_start: 0.7996 (mttm) cc_final: 0.7350 (mttp) REVERT: A 595 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: A 653 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 664 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6435 (mmp80) REVERT: A 679 LYS cc_start: 0.7855 (tttt) cc_final: 0.7092 (tttm) REVERT: A 730 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6978 (ttm-80) REVERT: A 787 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 882 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6836 (p90) outliers start: 28 outliers final: 16 residues processed: 85 average time/residue: 1.2484 time to fit residues: 111.4835 Evaluate side-chains 84 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6233 Z= 0.169 Angle : 0.512 9.247 8537 Z= 0.245 Chirality : 0.039 0.145 970 Planarity : 0.003 0.036 997 Dihedral : 13.907 93.202 1143 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.93 % Allowed : 19.24 % Favored : 75.82 % 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: 680 helix: 2.50 (0.29), residues: 307 sheet: -1.68 (0.46), residues: 100 loop : -1.64 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 PHE 0.019 0.001 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.007 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: A 503 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 593 LYS cc_start: 0.8004 (mttm) cc_final: 0.7354 (mttp) REVERT: A 595 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: A 653 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7932 (pp) REVERT: A 679 LYS cc_start: 0.7900 (tttt) cc_final: 0.7136 (tttm) REVERT: A 730 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6931 (ttm-80) REVERT: A 787 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: A 882 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6819 (p90) outliers start: 30 outliers final: 17 residues processed: 85 average time/residue: 1.3327 time to fit residues: 118.5437 Evaluate side-chains 83 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 451 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6233 Z= 0.206 Angle : 0.526 9.576 8537 Z= 0.254 Chirality : 0.040 0.143 970 Planarity : 0.003 0.036 997 Dihedral : 13.959 100.740 1143 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.77 % Allowed : 19.24 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 680 helix: 2.45 (0.29), residues: 308 sheet: -1.89 (0.46), residues: 104 loop : -1.57 (0.35), residues: 268 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 0.021 0.002 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.007 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: A 503 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 593 LYS cc_start: 0.7994 (mttm) cc_final: 0.7339 (mttp) REVERT: A 595 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6786 (tt0) REVERT: A 613 ASP cc_start: 0.7321 (t0) cc_final: 0.7043 (t70) REVERT: A 653 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 679 LYS cc_start: 0.7961 (tttt) cc_final: 0.7216 (tttm) REVERT: A 730 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7525 (ttm-80) REVERT: A 787 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 882 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6795 (p90) outliers start: 29 outliers final: 18 residues processed: 85 average time/residue: 1.2342 time to fit residues: 110.0908 Evaluate side-chains 86 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 62 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 451 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6233 Z= 0.156 Angle : 0.514 8.993 8537 Z= 0.244 Chirality : 0.039 0.142 970 Planarity : 0.003 0.036 997 Dihedral : 13.916 107.143 1143 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.26 % Allowed : 18.91 % Favored : 75.82 % 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: 0.47 (0.33), residues: 680 helix: 2.59 (0.29), residues: 307 sheet: -1.89 (0.45), residues: 104 loop : -1.53 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.002 0.000 HIS A 317 PHE 0.018 0.001 PHE A 853 TYR 0.014 0.001 TYR A 566 ARG 0.005 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 58 time to evaluate : 0.744 Fit side-chains REVERT: A 425 ASP cc_start: 0.7539 (t0) cc_final: 0.7158 (t0) REVERT: A 479 MET cc_start: 0.8744 (ttm) cc_final: 0.8474 (mtm) REVERT: A 498 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: A 503 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 593 LYS cc_start: 0.7980 (mttm) cc_final: 0.7332 (mttp) REVERT: A 595 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: A 653 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7931 (pp) REVERT: A 664 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6419 (mmp80) REVERT: A 679 LYS cc_start: 0.7898 (tttt) cc_final: 0.7130 (tttm) REVERT: A 730 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6948 (ttm-80) REVERT: A 787 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: A 853 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6375 (p90) REVERT: A 882 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6844 (p90) outliers start: 32 outliers final: 17 residues processed: 82 average time/residue: 1.2455 time to fit residues: 107.1823 Evaluate side-chains 82 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 457 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6233 Z= 0.129 Angle : 0.500 8.567 8537 Z= 0.235 Chirality : 0.038 0.145 970 Planarity : 0.003 0.036 997 Dihedral : 13.829 115.382 1143 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.29 % Allowed : 20.72 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.33), residues: 680 helix: 2.72 (0.29), residues: 307 sheet: -1.95 (0.45), residues: 106 loop : -1.44 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 908 HIS 0.001 0.000 HIS A 317 PHE 0.015 0.001 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.005 0.000 ARG A 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.7518 (tmm-80) cc_final: 0.7308 (ttp-170) REVERT: A 425 ASP cc_start: 0.7529 (t0) cc_final: 0.7147 (t0) REVERT: A 503 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 593 LYS cc_start: 0.7999 (mttm) cc_final: 0.7425 (mttp) REVERT: A 653 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7964 (pp) REVERT: A 679 LYS cc_start: 0.7901 (tttt) cc_final: 0.7120 (tttm) REVERT: A 730 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6913 (ttm-80) REVERT: A 787 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 853 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 882 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6911 (p90) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 1.2496 time to fit residues: 106.8911 Evaluate side-chains 81 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 730 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 451 GLN A 495 ASN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.128577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100808 restraints weight = 6212.601| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.74 r_work: 0.2806 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6233 Z= 0.211 Angle : 0.544 9.777 8537 Z= 0.259 Chirality : 0.040 0.153 970 Planarity : 0.003 0.035 997 Dihedral : 13.932 121.246 1143 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.61 % Allowed : 19.41 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.33), residues: 680 helix: 2.55 (0.29), residues: 308 sheet: -1.85 (0.46), residues: 104 loop : -1.44 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 381 PHE 0.021 0.002 PHE A 853 TYR 0.013 0.001 TYR A 566 ARG 0.005 0.000 ARG A 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2540.76 seconds wall clock time: 46 minutes 18.40 seconds (2778.40 seconds total)