Starting phenix.real_space_refine on Tue Sep 24 14:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axb_15698/09_2024/8axb_15698.cif" } resolution = 2.87 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= 0.024 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: 5 Type Number sf(0) Gaussians P 229 5.49 5 S 10 5.16 5 C 4397 2.51 5 N 1501 2.21 5 O 2246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8383 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3485 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 17, 'TRANS': 412} Chain breaks: 2 Chain: "B" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4896 Classifications: {'RNA': 230} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 97, 'rna3p_pyr': 95} Link IDs: {'rna2p': 38, 'rna3p': 191} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.17, per 1000 atoms: 0.74 Number of scatterers: 8383 At special positions: 0 Unit cell: (104, 94.016, 121.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 229 15.00 O 2246 8.00 N 1501 7.00 C 4397 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 - 3.00 Amino acid : True - 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: 2.21 Conformation dependent library (CDL) restraints added in 456.3 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 54.4% alpha, 11.9% beta 64 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.843A pdb=" N TRP A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.570A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.905A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.795A pdb=" N ARG A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 484 through 505 removed outlier: 3.966A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.573A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.658A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.933A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'A' and resid 618 through 635 removed outlier: 3.691A pdb=" N LEU A 635 " --> pdb=" O TYR A 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.820A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.421A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 450 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 609 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 545 " --> pdb=" O GLU A 609 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 164 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1490 1.33 - 1.45: 3396 1.45 - 1.57: 3675 1.57 - 1.69: 458 1.69 - 1.81: 14 Bond restraints: 9033 Sorted by residual: bond pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG ARG A 17 " pdb=" CD ARG A 17 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CA GLN A 64 " pdb=" C GLN A 64 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.55e-01 bond pdb=" CG1 ILE A 477 " pdb=" CD1 ILE A 477 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.43e-01 bond pdb=" CB ASP A 465 " pdb=" CG ASP A 465 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.34e-01 ... (remaining 9028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 13035 1.74 - 3.48: 255 3.48 - 5.22: 35 5.22 - 6.96: 7 6.96 - 8.70: 3 Bond angle restraints: 13335 Sorted by residual: angle pdb=" CA GLN A 64 " pdb=" CB GLN A 64 " pdb=" CG GLN A 64 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N GLN A 64 " pdb=" CA GLN A 64 " pdb=" C GLN A 64 " ideal model delta sigma weight residual 109.81 117.22 -7.41 2.21e+00 2.05e-01 1.13e+01 angle pdb=" CA GLN A 41 " pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.61e+00 angle pdb=" C LEU A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.37e+00 angle pdb=" CA LEU A 27 " pdb=" CB LEU A 27 " pdb=" CG LEU A 27 " ideal model delta sigma weight residual 116.30 125.00 -8.70 3.50e+00 8.16e-02 6.18e+00 ... (remaining 13330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.37: 4609 23.37 - 46.73: 674 46.73 - 70.10: 368 70.10 - 93.47: 80 93.47 - 116.83: 4 Dihedral angle restraints: 5735 sinusoidal: 4485 harmonic: 1250 Sorted by residual: dihedral pdb=" CA PHE A 433 " pdb=" C PHE A 433 " pdb=" N GLU A 434 " pdb=" CA GLU A 434 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" O4' A B 160 " pdb=" C1' A B 160 " pdb=" N9 A B 160 " pdb=" C4 A B 160 " ideal model delta sinusoidal sigma weight residual -90.00 -16.96 -73.04 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1392 0.044 - 0.087: 226 0.087 - 0.131: 41 0.131 - 0.175: 6 0.175 - 0.218: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA GLN A 64 " pdb=" N GLN A 64 " pdb=" C GLN A 64 " pdb=" CB GLN A 64 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" C1' C B 109 " pdb=" O4' C B 109 " pdb=" C2' C B 109 " pdb=" N1 C B 109 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1663 not shown) Planarity restraints: 852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 524 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" CG ASP A 524 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 524 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 524 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 157 " -0.027 2.00e-02 2.50e+03 1.39e-02 5.31e+00 pdb=" N9 A B 157 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 157 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 157 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 157 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 157 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 157 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 157 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 281 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.23e+00 pdb=" N PRO A 282 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 849 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 190 2.61 - 3.18: 6955 3.18 - 3.75: 16618 3.75 - 4.33: 20953 4.33 - 4.90: 29103 Nonbonded interactions: 73819 Sorted by model distance: nonbonded pdb=" O LEU A 54 " pdb=" OH TYR A 91 " model vdw 2.036 3.040 nonbonded pdb=" O6 G B 108 " pdb=" O2 U B 183 " model vdw 2.046 2.432 nonbonded pdb=" N2 G B 168 " pdb=" O2 C B 174 " model vdw 2.067 2.496 nonbonded pdb=" NE2 GLN A 580 " pdb=" O2' G B 12 " model vdw 2.140 3.120 nonbonded pdb=" N2 G B 105 " pdb=" O2 C B 186 " model vdw 2.163 2.496 ... (remaining 73814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.270 Find NCS groups from input model: 0.060 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 0.037 9033 Z= 0.225 Angle : 0.620 8.704 13335 Z= 0.312 Chirality : 0.034 0.218 1666 Planarity : 0.005 0.057 852 Dihedral : 23.868 116.831 4927 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.53 % Allowed : 33.60 % Favored : 65.87 % 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: -0.94 (0.42), residues: 424 helix: 0.28 (0.37), residues: 191 sheet: -1.70 (0.58), residues: 77 loop : -1.00 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 PHE 0.016 0.002 PHE A 305 TYR 0.010 0.002 TYR A 89 ARG 0.005 0.001 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 64 GLN cc_start: 0.6799 (pm20) cc_final: 0.6588 (pm20) REVERT: A 625 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7062 (tm-30) outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 1.3312 time to fit residues: 83.5568 Evaluate side-chains 38 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 494 GLN A 560 GLN A 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9033 Z= 0.294 Angle : 0.662 7.746 13335 Z= 0.334 Chirality : 0.036 0.193 1666 Planarity : 0.006 0.053 852 Dihedral : 23.655 119.747 4051 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.94 % Allowed : 28.57 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.42), residues: 424 helix: 0.22 (0.35), residues: 205 sheet: -1.74 (0.56), residues: 78 loop : -0.90 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 366 HIS 0.004 0.001 HIS A 500 PHE 0.015 0.003 PHE A 514 TYR 0.015 0.002 TYR A 581 ARG 0.009 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 40 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6755 (pmt170) REVERT: A 565 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: A 618 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7452 (p) REVERT: A 625 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7010 (tm-30) outliers start: 30 outliers final: 7 residues processed: 65 average time/residue: 1.0078 time to fit residues: 70.7885 Evaluate side-chains 45 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9033 Z= 0.379 Angle : 0.719 7.913 13335 Z= 0.361 Chirality : 0.038 0.185 1666 Planarity : 0.006 0.051 852 Dihedral : 23.762 120.337 4051 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 7.14 % Allowed : 29.10 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.41), residues: 424 helix: 0.14 (0.35), residues: 205 sheet: -1.84 (0.57), residues: 78 loop : -0.86 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 366 HIS 0.007 0.002 HIS A 500 PHE 0.018 0.003 PHE A 514 TYR 0.018 0.002 TYR A 474 ARG 0.005 0.001 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 39 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5316 (t80) REVERT: A 564 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7301 (mm-30) REVERT: A 565 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6922 (mp10) outliers start: 27 outliers final: 9 residues processed: 61 average time/residue: 0.9745 time to fit residues: 64.2798 Evaluate side-chains 47 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 61 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 584 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9033 Z= 0.185 Angle : 0.592 6.696 13335 Z= 0.297 Chirality : 0.033 0.225 1666 Planarity : 0.005 0.059 852 Dihedral : 23.590 119.431 4051 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.08 % Allowed : 29.10 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.41), residues: 424 helix: 0.56 (0.35), residues: 206 sheet: -1.63 (0.57), residues: 77 loop : -0.48 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 PHE 0.014 0.002 PHE A 433 TYR 0.017 0.002 TYR A 590 ARG 0.005 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 28 ASN cc_start: 0.6314 (OUTLIER) cc_final: 0.6008 (t0) REVERT: A 89 TYR cc_start: 0.5645 (OUTLIER) cc_final: 0.5283 (t80) REVERT: A 565 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: A 625 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6884 (tm-30) outliers start: 23 outliers final: 8 residues processed: 61 average time/residue: 1.2713 time to fit residues: 82.9945 Evaluate side-chains 50 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9033 Z= 0.223 Angle : 0.606 6.505 13335 Z= 0.305 Chirality : 0.033 0.187 1666 Planarity : 0.004 0.053 852 Dihedral : 23.579 119.427 4050 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.67 % Allowed : 28.04 % Favored : 64.29 % 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: -0.28 (0.42), residues: 424 helix: 0.65 (0.34), residues: 206 sheet: -1.54 (0.57), residues: 77 loop : -0.39 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 366 HIS 0.004 0.001 HIS A 500 PHE 0.013 0.002 PHE A 433 TYR 0.010 0.002 TYR A 590 ARG 0.004 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 37 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.5198 (t80) REVERT: A 298 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7641 (ttmt) REVERT: A 565 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: A 625 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6868 (tm-30) outliers start: 29 outliers final: 12 residues processed: 61 average time/residue: 0.9037 time to fit residues: 60.1086 Evaluate side-chains 51 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9033 Z= 0.197 Angle : 0.587 6.933 13335 Z= 0.294 Chirality : 0.032 0.200 1666 Planarity : 0.004 0.055 852 Dihedral : 23.546 119.164 4050 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.61 % Allowed : 29.63 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.42), residues: 424 helix: 0.81 (0.34), residues: 205 sheet: -1.43 (0.57), residues: 77 loop : -0.22 (0.61), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 PHE 0.013 0.002 PHE A 433 TYR 0.008 0.001 TYR A 581 ARG 0.003 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 37 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.5222 (t80) REVERT: A 298 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (ttmt) REVERT: A 565 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7022 (mp10) outliers start: 25 outliers final: 12 residues processed: 58 average time/residue: 0.8560 time to fit residues: 54.6312 Evaluate side-chains 51 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 595 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9033 Z= 0.164 Angle : 0.571 8.169 13335 Z= 0.285 Chirality : 0.031 0.171 1666 Planarity : 0.004 0.055 852 Dihedral : 23.483 118.770 4050 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.56 % Allowed : 29.89 % Favored : 64.55 % 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: 0.14 (0.43), residues: 424 helix: 0.94 (0.35), residues: 205 sheet: -1.16 (0.58), residues: 76 loop : -0.21 (0.62), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.016 0.002 PHE A 13 TYR 0.031 0.002 TYR A 474 ARG 0.004 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5302 (t80) REVERT: A 298 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7548 (ttmt) REVERT: A 565 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7115 (mp10) outliers start: 21 outliers final: 9 residues processed: 56 average time/residue: 1.0351 time to fit residues: 62.6573 Evaluate side-chains 47 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9033 Z= 0.278 Angle : 0.648 9.717 13335 Z= 0.321 Chirality : 0.034 0.218 1666 Planarity : 0.005 0.054 852 Dihedral : 23.569 118.938 4050 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.08 % Allowed : 29.63 % Favored : 64.29 % 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 (0.42), residues: 424 helix: 0.76 (0.35), residues: 205 sheet: -1.37 (0.58), residues: 77 loop : -0.29 (0.61), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 366 HIS 0.005 0.001 HIS A 500 PHE 0.014 0.002 PHE A 514 TYR 0.025 0.002 TYR A 474 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 37 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 565 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: A 625 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6870 (tm-30) outliers start: 23 outliers final: 13 residues processed: 57 average time/residue: 0.8952 time to fit residues: 55.6782 Evaluate side-chains 51 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 595 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9033 Z= 0.317 Angle : 0.690 12.120 13335 Z= 0.342 Chirality : 0.036 0.184 1666 Planarity : 0.005 0.052 852 Dihedral : 23.682 119.303 4050 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.76 % Allowed : 31.75 % Favored : 63.49 % 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: -0.38 (0.41), residues: 424 helix: 0.53 (0.34), residues: 205 sheet: -1.52 (0.56), residues: 77 loop : -0.41 (0.60), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 366 HIS 0.009 0.002 HIS A 369 PHE 0.017 0.002 PHE A 13 TYR 0.024 0.002 TYR A 474 ARG 0.008 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5283 (t80) REVERT: A 565 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 625 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6950 (tm-30) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 0.8405 time to fit residues: 51.5790 Evaluate side-chains 52 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9033 Z= 0.189 Angle : 0.626 13.206 13335 Z= 0.310 Chirality : 0.033 0.186 1666 Planarity : 0.004 0.056 852 Dihedral : 23.562 119.095 4050 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.70 % Allowed : 33.86 % Favored : 62.43 % 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: -0.03 (0.42), residues: 424 helix: 0.80 (0.35), residues: 205 sheet: -1.31 (0.57), residues: 77 loop : -0.23 (0.61), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 366 HIS 0.010 0.001 HIS A 42 PHE 0.012 0.001 PHE A 325 TYR 0.022 0.002 TYR A 474 ARG 0.007 0.001 ARG A 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.589 Fit side-chains REVERT: A 89 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.5300 (t80) REVERT: A 565 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: A 625 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6885 (tm-30) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.9596 time to fit residues: 53.3597 Evaluate side-chains 49 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.139721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.113749 restraints weight = 21720.818| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.16 r_work: 0.4008 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9033 Z= 0.166 Angle : 0.595 10.274 13335 Z= 0.295 Chirality : 0.032 0.209 1666 Planarity : 0.004 0.053 852 Dihedral : 23.456 118.352 4050 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.17 % Allowed : 33.86 % Favored : 62.96 % 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: 0.19 (0.43), residues: 424 helix: 0.93 (0.35), residues: 203 sheet: -1.06 (0.58), residues: 76 loop : -0.14 (0.63), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 366 HIS 0.004 0.001 HIS A 369 PHE 0.024 0.002 PHE A 13 TYR 0.021 0.002 TYR A 590 ARG 0.007 0.001 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.53 seconds wall clock time: 43 minutes 32.32 seconds (2612.32 seconds total)