Starting phenix.real_space_refine on Sun Mar 10 22:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/03_2024/8ooy_17033.pdb" } resolution = 4.0 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= 0.001 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 51 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3520 2.51 5 N 1029 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5828 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: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Chain: "T" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} 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: 3.76, per 1000 atoms: 0.65 Number of scatterers: 5828 At special positions: 0 Unit cell: (89.452, 96.14, 78.584, 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 51 15.00 Mg 1 11.99 O 1212 8.00 N 1029 7.00 C 3520 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: 2.75 Conformation dependent library (CDL) restraints added in 1.0 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: 28 helices and 4 sheets defined 62.7% alpha, 5.6% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.673A pdb=" N LYS A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.605A pdb=" N ASP A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.944A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.045A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLN A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Proline residue: A 514 - end of helix removed outlier: 3.555A pdb=" N HIS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.405A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.831A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.628A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.032A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.799A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.877A pdb=" N ILE A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 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 Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 750 through 767 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 812 removed outlier: 3.734A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 871 removed outlier: 3.743A 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 892 through 906 removed outlier: 3.570A pdb=" N ALA A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.620A pdb=" N TYR A 382 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.262A pdb=" N PHE A 352 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.587A pdb=" N SER A 670 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 702 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1534 1.33 - 1.45: 1226 1.45 - 1.57: 3153 1.57 - 1.69: 99 1.69 - 1.81: 29 Bond restraints: 6041 Sorted by residual: bond pdb=" N VAL A 663 " pdb=" CA VAL A 663 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.48e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.88e+00 bond pdb=" N VAL A 504 " pdb=" CA VAL A 504 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.17e-02 7.31e+03 5.56e+00 bond pdb=" N ASP A 501 " pdb=" CA ASP A 501 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.41e+00 bond pdb=" N THR A 485 " pdb=" CA THR A 485 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.25e-02 6.40e+03 4.83e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.31: 297 105.31 - 112.48: 3175 112.48 - 119.64: 2085 119.64 - 126.80: 2641 126.80 - 133.96: 193 Bond angle restraints: 8391 Sorted by residual: angle pdb=" CA THR A 664 " pdb=" C THR A 664 " pdb=" O THR A 664 " ideal model delta sigma weight residual 121.56 117.76 3.80 1.09e+00 8.42e-01 1.21e+01 angle pdb=" CA LEU A 506 " pdb=" C LEU A 506 " pdb=" O LEU A 506 " ideal model delta sigma weight residual 120.90 117.30 3.60 1.07e+00 8.73e-01 1.13e+01 angle pdb=" C ASN A 554 " pdb=" N HIS A 555 " pdb=" CA HIS A 555 " ideal model delta sigma weight residual 120.28 125.04 -4.76 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 112.12 109.38 2.74 8.40e-01 1.42e+00 1.06e+01 angle pdb=" N THR A 505 " pdb=" CA THR A 505 " pdb=" C THR A 505 " ideal model delta sigma weight residual 111.11 107.33 3.78 1.20e+00 6.94e-01 9.94e+00 ... (remaining 8386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2879 17.28 - 34.57: 390 34.57 - 51.85: 194 51.85 - 69.13: 65 69.13 - 86.41: 7 Dihedral angle restraints: 3535 sinusoidal: 1772 harmonic: 1763 Sorted by residual: dihedral pdb=" CA VAL A 815 " pdb=" C VAL A 815 " pdb=" N GLU A 816 " pdb=" CA GLU A 816 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP A 892 " pdb=" CB ASP A 892 " pdb=" CG ASP A 892 " pdb=" OD1 ASP A 892 " ideal model delta sinusoidal sigma weight residual -30.00 -85.98 55.98 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " pdb=" CD GLU A 917 " pdb=" OE1 GLU A 917 " ideal model delta sinusoidal sigma weight residual 0.00 86.41 -86.41 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 694 0.042 - 0.083: 179 0.083 - 0.125: 64 0.125 - 0.167: 5 0.167 - 0.208: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 941 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 521 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 522 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 779 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 780 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 901 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C HIS A 901 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS A 901 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 902 " -0.009 2.00e-02 2.50e+03 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5044 3.17 - 3.75: 10010 3.75 - 4.32: 13143 4.32 - 4.90: 20807 Nonbonded interactions: 49064 Sorted by model distance: nonbonded pdb=" OD1 ASP A 355 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.201 2.520 nonbonded pdb=" NE2 HIS A 555 " pdb=" OE2 GLU A 685 " model vdw 2.206 2.520 nonbonded pdb=" OE1 GLU A 729 " pdb=" NZ LYS A 731 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 817 " pdb=" OG1 THR A 851 " model vdw 2.231 2.440 ... (remaining 49059 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: 0.690 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: 3.600 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.004 0.039 6041 Z= 0.219 Angle : 0.681 7.727 8391 Z= 0.395 Chirality : 0.043 0.208 944 Planarity : 0.004 0.045 913 Dihedral : 20.016 86.412 2395 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.79 % Allowed : 0.39 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.97 (0.35), residues: 602 helix: 0.59 (0.30), residues: 315 sheet: -3.34 (0.66), residues: 47 loop : -1.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 465 HIS 0.011 0.001 HIS A 555 PHE 0.016 0.002 PHE A 354 TYR 0.015 0.001 TYR A 814 ARG 0.006 0.001 ARG A 806 *********************** 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 77 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 679 ILE cc_start: 0.8365 (mm) cc_final: 0.8088 (mm) REVERT: A 848 MET cc_start: 0.7810 (mmm) cc_final: 0.7187 (mmm) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1588 time to fit residues: 16.6564 Evaluate side-chains 53 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.197 Angle : 0.600 8.209 8391 Z= 0.320 Chirality : 0.041 0.192 944 Planarity : 0.005 0.051 913 Dihedral : 21.713 66.272 1200 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.97 % Allowed : 8.27 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.58 (0.35), residues: 602 helix: 0.88 (0.29), residues: 325 sheet: -3.24 (0.64), residues: 49 loop : -1.52 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 342 HIS 0.007 0.001 HIS A 555 PHE 0.016 0.001 PHE A 886 TYR 0.020 0.001 TYR A 814 ARG 0.005 0.000 ARG A 806 *********************** 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 70 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8375 (mt) cc_final: 0.8092 (mt) REVERT: A 449 LEU cc_start: 0.8836 (mt) cc_final: 0.8570 (mt) REVERT: A 506 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 679 ILE cc_start: 0.8309 (mm) cc_final: 0.8012 (mm) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.1504 time to fit residues: 14.0788 Evaluate side-chains 56 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 760 ILE 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: 0.9980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6041 Z= 0.191 Angle : 0.563 7.760 8391 Z= 0.302 Chirality : 0.039 0.165 944 Planarity : 0.004 0.048 913 Dihedral : 21.674 64.415 1200 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.36 % Allowed : 12.01 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.28 (0.36), residues: 602 helix: 1.06 (0.29), residues: 326 sheet: -3.12 (0.71), residues: 44 loop : -1.35 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 866 HIS 0.005 0.001 HIS A 555 PHE 0.016 0.001 PHE A 886 TYR 0.018 0.001 TYR A 814 ARG 0.004 0.000 ARG A 806 *********************** 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 73 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8391 (mt) cc_final: 0.8101 (mt) REVERT: A 449 LEU cc_start: 0.8839 (mt) cc_final: 0.8562 (mt) REVERT: A 506 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 679 ILE cc_start: 0.8288 (mm) cc_final: 0.8003 (mm) REVERT: A 768 MET cc_start: 0.7638 (ppp) cc_final: 0.7314 (ppp) REVERT: A 788 MET cc_start: 0.7477 (mtm) cc_final: 0.7186 (mtm) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.1504 time to fit residues: 14.4758 Evaluate side-chains 60 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.202 Angle : 0.555 7.758 8391 Z= 0.298 Chirality : 0.039 0.160 944 Planarity : 0.004 0.046 913 Dihedral : 21.744 66.820 1200 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.15 % Allowed : 14.76 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.35), residues: 602 helix: 1.15 (0.29), residues: 326 sheet: -3.29 (0.62), residues: 44 loop : -1.26 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 866 HIS 0.003 0.001 HIS A 901 PHE 0.014 0.002 PHE A 886 TYR 0.018 0.001 TYR A 814 ARG 0.003 0.000 ARG A 682 *********************** 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 69 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8370 (mt) cc_final: 0.8104 (mt) REVERT: A 449 LEU cc_start: 0.8860 (mt) cc_final: 0.8631 (mt) REVERT: A 463 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: A 506 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 679 ILE cc_start: 0.8382 (mm) cc_final: 0.8102 (mm) REVERT: A 768 MET cc_start: 0.7700 (ppp) cc_final: 0.7301 (ppp) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1757 time to fit residues: 15.9394 Evaluate side-chains 62 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6041 Z= 0.257 Angle : 0.589 8.364 8391 Z= 0.313 Chirality : 0.040 0.169 944 Planarity : 0.005 0.046 913 Dihedral : 21.899 74.144 1200 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.54 % Allowed : 15.75 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.34 (0.35), residues: 602 helix: 1.02 (0.29), residues: 324 sheet: -3.24 (0.61), residues: 44 loop : -1.36 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 342 HIS 0.005 0.001 HIS A 901 PHE 0.014 0.002 PHE A 792 TYR 0.019 0.002 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** 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 73 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: A 506 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 679 ILE cc_start: 0.8518 (mm) cc_final: 0.8255 (mm) outliers start: 18 outliers final: 12 residues processed: 68 average time/residue: 0.1781 time to fit residues: 16.3868 Evaluate side-chains 62 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.186 Angle : 0.566 8.068 8391 Z= 0.301 Chirality : 0.039 0.173 944 Planarity : 0.004 0.046 913 Dihedral : 21.919 76.040 1200 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.95 % Allowed : 16.93 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.19 (0.35), residues: 602 helix: 1.07 (0.29), residues: 328 sheet: -3.09 (0.60), residues: 44 loop : -1.21 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 866 HIS 0.008 0.001 HIS A 901 PHE 0.017 0.002 PHE A 792 TYR 0.017 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** 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 76 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 463 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: A 506 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 679 ILE cc_start: 0.8486 (mm) cc_final: 0.8247 (mm) REVERT: A 755 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8116 (ppt170) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1705 time to fit residues: 16.3195 Evaluate side-chains 63 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6041 Z= 0.326 Angle : 0.650 10.958 8391 Z= 0.342 Chirality : 0.042 0.195 944 Planarity : 0.005 0.046 913 Dihedral : 22.079 79.912 1200 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.54 % Allowed : 17.32 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.46 (0.35), residues: 602 helix: 0.86 (0.29), residues: 324 sheet: -2.88 (0.66), residues: 43 loop : -1.41 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 342 HIS 0.005 0.001 HIS A 901 PHE 0.019 0.002 PHE A 792 TYR 0.021 0.002 TYR A 814 ARG 0.004 0.001 ARG A 682 *********************** 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 74 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8389 (mt) cc_final: 0.8058 (mt) REVERT: A 463 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: A 506 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8324 (mm) REVERT: A 755 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8080 (ppt170) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.1786 time to fit residues: 16.9637 Evaluate side-chains 66 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 507 GLN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6041 Z= 0.193 Angle : 0.602 9.922 8391 Z= 0.315 Chirality : 0.040 0.188 944 Planarity : 0.004 0.046 913 Dihedral : 22.034 81.350 1200 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.95 % Allowed : 18.50 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.35), residues: 602 helix: 1.06 (0.29), residues: 323 sheet: -2.88 (0.67), residues: 44 loop : -1.18 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 513 HIS 0.003 0.001 HIS A 901 PHE 0.020 0.002 PHE A 792 TYR 0.017 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** 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 71 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8330 (mt) cc_final: 0.8016 (mt) REVERT: A 463 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: A 506 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 661 GLN cc_start: 0.8333 (tt0) cc_final: 0.8115 (tt0) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1728 time to fit residues: 16.1965 Evaluate side-chains 64 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 815 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 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 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.191 Angle : 0.595 9.825 8391 Z= 0.312 Chirality : 0.039 0.189 944 Planarity : 0.004 0.047 913 Dihedral : 21.994 82.082 1200 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.15 % Allowed : 18.31 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.02 (0.35), residues: 602 helix: 1.14 (0.29), residues: 323 sheet: -2.46 (0.72), residues: 43 loop : -1.12 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 513 HIS 0.004 0.001 HIS A 901 PHE 0.022 0.002 PHE A 792 TYR 0.016 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 *********************** 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 74 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8302 (mt) cc_final: 0.7968 (mt) REVERT: A 463 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: A 661 GLN cc_start: 0.8305 (tt0) cc_final: 0.8077 (tt0) REVERT: A 788 MET cc_start: 0.6569 (mtm) cc_final: 0.5985 (mtm) outliers start: 16 outliers final: 12 residues processed: 70 average time/residue: 0.1719 time to fit residues: 16.3210 Evaluate side-chains 69 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 856 ILE 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: 0.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6041 Z= 0.215 Angle : 0.611 10.148 8391 Z= 0.323 Chirality : 0.040 0.187 944 Planarity : 0.004 0.046 913 Dihedral : 22.030 83.587 1200 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.56 % Allowed : 19.29 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.05 (0.35), residues: 602 helix: 1.08 (0.29), residues: 323 sheet: -2.31 (0.72), residues: 44 loop : -1.10 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 924 HIS 0.004 0.001 HIS A 901 PHE 0.020 0.002 PHE A 742 TYR 0.017 0.002 TYR A 814 ARG 0.004 0.000 ARG A 682 ********************** 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 71 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8340 (mt) cc_final: 0.8020 (mt) REVERT: A 427 ILE cc_start: 0.9080 (mt) cc_final: 0.8788 (tp) REVERT: A 463 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 661 GLN cc_start: 0.8325 (tt0) cc_final: 0.8097 (tt0) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.1730 time to fit residues: 15.6686 Evaluate side-chains 68 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084737 restraints weight = 14604.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084720 restraints weight = 11386.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085851 restraints weight = 10651.133| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6041 Z= 0.186 Angle : 0.598 9.988 8391 Z= 0.314 Chirality : 0.039 0.188 944 Planarity : 0.004 0.048 913 Dihedral : 21.992 84.873 1200 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.76 % Allowed : 19.29 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.35), residues: 602 helix: 1.12 (0.29), residues: 327 sheet: -1.87 (0.73), residues: 43 loop : -0.98 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 513 HIS 0.004 0.001 HIS A 901 PHE 0.017 0.002 PHE A 886 TYR 0.015 0.001 TYR A 814 ARG 0.004 0.000 ARG A 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1299.44 seconds wall clock time: 24 minutes 21.84 seconds (1461.84 seconds total)