Starting phenix.real_space_refine on Sun Mar 10 23:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oo6_17005/03_2024/8oo6_17005.pdb" } resolution = 4.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3549 2.51 5 N 1042 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5890 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 28, 'TRANS': 575} Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.66, per 1000 atoms: 0.62 Number of scatterers: 5890 At special positions: 0 Unit cell: (86.6, 96.992, 78.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 54 15.00 Mg 1 11.99 O 1229 8.00 N 1042 7.00 C 3549 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: 2.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 59.8% alpha, 7.5% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 397 through 410 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.659A pdb=" N TYR A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 472 through 477 removed outlier: 4.010A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.755A pdb=" N ILE A 489 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 517 removed outlier: 3.587A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Proline residue: A 514 - end of helix Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.231A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.886A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 621 through 644 removed outlier: 4.350A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.841A pdb=" N PHE A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.933A pdb=" N ALA A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 766 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 813 removed outlier: 3.650A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 871 removed outlier: 3.551A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.130A pdb=" N VAL A 331 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 371 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 352 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 875 through 880 removed outlier: 3.548A pdb=" N ILE A 877 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 885 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN A 879 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 883 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 702 " --> pdb=" O PHE A 886 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 816 261 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1376 1.33 - 1.45: 1384 1.45 - 1.57: 3217 1.57 - 1.69: 105 1.69 - 1.81: 29 Bond restraints: 6111 Sorted by residual: bond pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.31e-02 5.83e+03 1.86e+00 bond pdb=" CG LEU A 449 " pdb=" CD1 LEU A 449 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB ASP A 388 " pdb=" CG ASP A 388 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB PRO A 674 " pdb=" CG PRO A 674 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" CB LEU A 449 " pdb=" CG LEU A 449 " ideal model delta sigma weight residual 1.530 1.510 0.020 2.00e-02 2.50e+03 9.98e-01 ... (remaining 6106 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.47: 267 104.47 - 111.85: 3053 111.85 - 119.22: 2067 119.22 - 126.59: 2897 126.59 - 133.97: 215 Bond angle restraints: 8499 Sorted by residual: angle pdb=" N GLU A 629 " pdb=" CA GLU A 629 " pdb=" CB GLU A 629 " ideal model delta sigma weight residual 110.12 114.36 -4.24 1.47e+00 4.63e-01 8.33e+00 angle pdb=" CB MET A 714 " pdb=" CG MET A 714 " pdb=" SD MET A 714 " ideal model delta sigma weight residual 112.70 104.16 8.54 3.00e+00 1.11e-01 8.10e+00 angle pdb=" N ALA A 366 " pdb=" CA ALA A 366 " pdb=" C ALA A 366 " ideal model delta sigma weight residual 111.17 115.17 -4.00 1.41e+00 5.03e-01 8.06e+00 angle pdb=" N GLN A 507 " pdb=" CA GLN A 507 " pdb=" CB GLN A 507 " ideal model delta sigma weight residual 110.28 114.56 -4.28 1.55e+00 4.16e-01 7.62e+00 angle pdb=" N MET A 802 " pdb=" CA MET A 802 " pdb=" CB MET A 802 " ideal model delta sigma weight residual 110.12 113.89 -3.77 1.47e+00 4.63e-01 6.59e+00 ... (remaining 8494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2887 17.99 - 35.98: 419 35.98 - 53.96: 215 53.96 - 71.95: 41 71.95 - 89.94: 7 Dihedral angle restraints: 3569 sinusoidal: 1806 harmonic: 1763 Sorted by residual: dihedral pdb=" CA ASP A 705 " pdb=" C ASP A 705 " pdb=" N TYR A 706 " pdb=" CA TYR A 706 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N GLU A 347 " pdb=" CA GLU A 347 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU A 611 " pdb=" C GLU A 611 " pdb=" N GLU A 612 " pdb=" CA GLU A 612 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 678 0.035 - 0.070: 185 0.070 - 0.106: 79 0.106 - 0.141: 10 0.141 - 0.176: 4 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA MET A 531 " pdb=" N MET A 531 " pdb=" C MET A 531 " pdb=" CB MET A 531 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CG LEU A 884 " pdb=" CB LEU A 884 " pdb=" CD1 LEU A 884 " pdb=" CD2 LEU A 884 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA GLN A 507 " pdb=" N GLN A 507 " pdb=" C GLN A 507 " pdb=" CB GLN A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 953 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 465 " 0.017 2.00e-02 2.50e+03 1.47e-02 5.39e+00 pdb=" CG TRP A 465 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 465 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 465 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 465 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 465 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 465 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 465 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 465 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 465 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 392 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 393 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 388 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ASP A 388 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 388 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 389 " -0.011 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 910 2.76 - 3.29: 5838 3.29 - 3.83: 10831 3.83 - 4.36: 12008 4.36 - 4.90: 19050 Nonbonded interactions: 48637 Sorted by model distance: nonbonded pdb=" OG1 THR A 485 " pdb=" OD1 ASN A 487 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR A 358 " pdb=" O ASN A 367 " model vdw 2.241 2.440 nonbonded pdb=" ND2 ASN A 579 " pdb=" OP1 DA T 27 " model vdw 2.241 2.520 nonbonded pdb=" O GLN A 868 " pdb=" NE2 GLN A 871 " model vdw 2.270 2.520 nonbonded pdb=" NH2 ARG A 909 " pdb=" O LEU A 910 " model vdw 2.313 2.520 ... (remaining 48632 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 group one per residue 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.730 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.550 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.003 0.052 6111 Z= 0.203 Angle : 0.667 8.537 8499 Z= 0.374 Chirality : 0.039 0.176 956 Planarity : 0.004 0.054 916 Dihedral : 20.164 89.936 2429 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.09 (0.35), residues: 602 helix: 0.78 (0.29), residues: 321 sheet: -1.17 (0.85), residues: 41 loop : -0.92 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 465 HIS 0.003 0.001 HIS A 734 PHE 0.022 0.001 PHE A 762 TYR 0.012 0.001 TYR A 801 ARG 0.003 0.000 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.653 Fit side-chains REVERT: A 346 LEU cc_start: 0.9011 (mt) cc_final: 0.8758 (mt) REVERT: A 798 VAL cc_start: 0.9432 (t) cc_final: 0.9063 (t) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1327 time to fit residues: 7.1943 Evaluate side-chains 24 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6111 Z= 0.165 Angle : 0.549 6.497 8499 Z= 0.304 Chirality : 0.037 0.139 956 Planarity : 0.004 0.051 916 Dihedral : 22.195 59.834 1234 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.20 % Allowed : 5.91 % Favored : 93.90 % 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: 0.21 (0.35), residues: 602 helix: 1.15 (0.29), residues: 329 sheet: -0.68 (0.91), residues: 41 loop : -1.14 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 465 HIS 0.003 0.001 HIS A 327 PHE 0.010 0.001 PHE A 762 TYR 0.008 0.001 TYR A 630 ARG 0.002 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.600 Fit side-chains REVERT: A 346 LEU cc_start: 0.8963 (mt) cc_final: 0.8603 (mt) REVERT: A 559 LEU cc_start: 0.8991 (mt) cc_final: 0.8790 (mt) REVERT: A 798 VAL cc_start: 0.9442 (t) cc_final: 0.8831 (t) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1259 time to fit residues: 7.0848 Evaluate side-chains 24 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6111 Z= 0.220 Angle : 0.582 6.915 8499 Z= 0.322 Chirality : 0.039 0.156 956 Planarity : 0.004 0.045 916 Dihedral : 22.200 59.909 1234 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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: 0.04 (0.35), residues: 602 helix: 0.94 (0.29), residues: 333 sheet: -0.59 (0.89), residues: 41 loop : -1.17 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 465 HIS 0.005 0.001 HIS A 555 PHE 0.010 0.001 PHE A 771 TYR 0.011 0.002 TYR A 795 ARG 0.004 0.001 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 798 VAL cc_start: 0.9411 (t) cc_final: 0.9019 (t) REVERT: A 802 MET cc_start: 0.9204 (mpp) cc_final: 0.8998 (mpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1330 time to fit residues: 6.8046 Evaluate side-chains 21 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 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 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.003 0.043 6111 Z= 0.162 Angle : 0.560 6.283 8499 Z= 0.306 Chirality : 0.038 0.154 956 Planarity : 0.004 0.044 916 Dihedral : 22.184 60.108 1234 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 (0.35), residues: 602 helix: 1.11 (0.29), residues: 329 sheet: -0.56 (0.88), residues: 41 loop : -1.12 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 465 HIS 0.002 0.001 HIS A 734 PHE 0.010 0.001 PHE A 373 TYR 0.009 0.001 TYR A 497 ARG 0.001 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.601 Fit side-chains REVERT: A 798 VAL cc_start: 0.9462 (t) cc_final: 0.8975 (t) REVERT: A 802 MET cc_start: 0.9290 (mpp) cc_final: 0.9052 (mpp) REVERT: A 887 GLU cc_start: 0.8051 (tp30) cc_final: 0.7797 (tp30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1286 time to fit residues: 6.3912 Evaluate side-chains 22 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6111 Z= 0.377 Angle : 0.723 9.636 8499 Z= 0.396 Chirality : 0.043 0.156 956 Planarity : 0.005 0.041 916 Dihedral : 22.459 68.256 1234 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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: -0.54 (0.34), residues: 602 helix: 0.43 (0.28), residues: 334 sheet: -0.54 (0.84), residues: 41 loop : -1.44 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 866 HIS 0.005 0.002 HIS A 327 PHE 0.016 0.002 PHE A 771 TYR 0.020 0.002 TYR A 431 ARG 0.005 0.001 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.627 Fit side-chains REVERT: A 798 VAL cc_start: 0.9418 (t) cc_final: 0.9001 (t) REVERT: A 802 MET cc_start: 0.9295 (mpp) cc_final: 0.8941 (mpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1247 time to fit residues: 5.7697 Evaluate side-chains 21 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN A 543 ASN A 845 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6111 Z= 0.173 Angle : 0.597 6.311 8499 Z= 0.325 Chirality : 0.039 0.128 956 Planarity : 0.005 0.080 916 Dihedral : 22.355 68.311 1234 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.20 % Allowed : 1.97 % Favored : 97.83 % 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: -0.09 (0.35), residues: 602 helix: 0.86 (0.29), residues: 330 sheet: -0.50 (0.82), residues: 41 loop : -1.29 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 342 HIS 0.002 0.000 HIS A 734 PHE 0.008 0.001 PHE A 727 TYR 0.012 0.001 TYR A 497 ARG 0.002 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.610 Fit side-chains REVERT: A 713 ILE cc_start: 0.8988 (mm) cc_final: 0.8746 (mt) REVERT: A 798 VAL cc_start: 0.9439 (t) cc_final: 0.9044 (t) REVERT: A 802 MET cc_start: 0.9392 (mpp) cc_final: 0.9086 (mpp) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1390 time to fit residues: 6.0238 Evaluate side-chains 23 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6111 Z= 0.195 Angle : 0.582 7.003 8499 Z= 0.318 Chirality : 0.039 0.156 956 Planarity : 0.004 0.067 916 Dihedral : 22.276 70.950 1234 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 0.03 (0.35), residues: 602 helix: 1.00 (0.29), residues: 333 sheet: -0.46 (0.81), residues: 41 loop : -1.34 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.002 0.001 HIS A 555 PHE 0.009 0.001 PHE A 771 TYR 0.009 0.001 TYR A 497 ARG 0.002 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 512 MET cc_start: 0.8793 (ttp) cc_final: 0.8506 (ttp) REVERT: A 713 ILE cc_start: 0.9007 (mm) cc_final: 0.8751 (mt) REVERT: A 798 VAL cc_start: 0.9397 (t) cc_final: 0.9017 (t) REVERT: A 802 MET cc_start: 0.9398 (mpp) cc_final: 0.9028 (mpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1392 time to fit residues: 6.2849 Evaluate side-chains 23 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6111 Z= 0.164 Angle : 0.559 6.205 8499 Z= 0.306 Chirality : 0.038 0.124 956 Planarity : 0.004 0.057 916 Dihedral : 22.221 70.907 1234 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 0.11 (0.35), residues: 602 helix: 1.03 (0.29), residues: 334 sheet: -0.37 (0.81), residues: 41 loop : -1.26 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.002 0.001 HIS A 555 PHE 0.006 0.001 PHE A 771 TYR 0.009 0.001 TYR A 497 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 512 MET cc_start: 0.8786 (ttp) cc_final: 0.8467 (ttp) REVERT: A 798 VAL cc_start: 0.9388 (t) cc_final: 0.9011 (t) REVERT: A 802 MET cc_start: 0.9432 (mpp) cc_final: 0.9080 (mpp) REVERT: A 845 ASN cc_start: 0.8753 (t0) cc_final: 0.8545 (t0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1378 time to fit residues: 6.5384 Evaluate side-chains 25 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.0270 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6111 Z= 0.159 Angle : 0.568 6.707 8499 Z= 0.309 Chirality : 0.038 0.130 956 Planarity : 0.004 0.049 916 Dihedral : 22.144 71.083 1234 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.35), residues: 602 helix: 1.16 (0.29), residues: 331 sheet: -0.11 (0.83), residues: 41 loop : -1.22 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 342 HIS 0.002 0.000 HIS A 555 PHE 0.005 0.001 PHE A 771 TYR 0.008 0.001 TYR A 497 ARG 0.003 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 512 MET cc_start: 0.8805 (ttp) cc_final: 0.8485 (ttp) REVERT: A 798 VAL cc_start: 0.9412 (t) cc_final: 0.8968 (t) REVERT: A 802 MET cc_start: 0.9452 (mpp) cc_final: 0.9083 (mpp) REVERT: A 845 ASN cc_start: 0.8828 (t0) cc_final: 0.8538 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1613 time to fit residues: 7.6912 Evaluate side-chains 24 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6111 Z= 0.178 Angle : 0.580 6.113 8499 Z= 0.318 Chirality : 0.038 0.158 956 Planarity : 0.004 0.046 916 Dihedral : 22.104 71.862 1234 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.35), residues: 602 helix: 1.06 (0.29), residues: 334 sheet: 0.12 (0.83), residues: 41 loop : -1.20 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 924 HIS 0.002 0.001 HIS A 734 PHE 0.010 0.001 PHE A 373 TYR 0.010 0.001 TYR A 706 ARG 0.001 0.000 ARG A 873 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 512 MET cc_start: 0.8864 (ttp) cc_final: 0.8574 (ttp) REVERT: A 798 VAL cc_start: 0.9449 (t) cc_final: 0.8985 (m) REVERT: A 802 MET cc_start: 0.9442 (mpp) cc_final: 0.9088 (mpp) REVERT: A 845 ASN cc_start: 0.8863 (t0) cc_final: 0.8368 (m-40) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1303 time to fit residues: 6.8416 Evaluate side-chains 25 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.0570 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041768 restraints weight = 38468.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042956 restraints weight = 20987.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043747 restraints weight = 14052.852| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6111 Z= 0.169 Angle : 0.578 6.673 8499 Z= 0.315 Chirality : 0.039 0.159 956 Planarity : 0.004 0.043 916 Dihedral : 22.069 71.953 1234 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.35), residues: 602 helix: 1.07 (0.29), residues: 335 sheet: 0.28 (0.83), residues: 41 loop : -1.19 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 342 HIS 0.001 0.001 HIS A 656 PHE 0.006 0.001 PHE A 771 TYR 0.008 0.001 TYR A 630 ARG 0.002 0.000 ARG A 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.27 seconds wall clock time: 23 minutes 22.16 seconds (1402.16 seconds total)