Starting phenix.real_space_refine on Thu Nov 14 00:00:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8p_16490/11_2024/8c8p_16490.cif" } resolution = 4.1 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= 0.002 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1564 2.51 5 N 409 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2449 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 2.79, per 1000 atoms: 1.14 Number of scatterers: 2449 At special positions: 0 Unit cell: (60.1938, 67.9967, 85.8319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 464 8.00 N 409 7.00 C 1564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 0.63 Conformation dependent library (CDL) restraints added in 299.0 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 566 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 13.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.775A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.901A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.677A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.008A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.733A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.682A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER H 21 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.420A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA H 96 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.232A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 57 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 785 1.34 - 1.46: 673 1.46 - 1.58: 1041 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2513 Sorted by residual: bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.56e+00 bond pdb=" CA ASN H 76 " pdb=" CB ASN H 76 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.54e-02 4.22e+03 1.40e+00 bond pdb=" CA VAL H 118 " pdb=" CB VAL H 118 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.01e-01 bond pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.61e-01 bond pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta sigma weight residual 1.458 1.451 0.007 9.20e-03 1.18e+04 6.27e-01 ... (remaining 2508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3330 1.82 - 3.64: 71 3.64 - 5.46: 9 5.46 - 7.29: 4 7.29 - 9.11: 1 Bond angle restraints: 3415 Sorted by residual: angle pdb=" C LYS H 75 " pdb=" N ASN H 76 " pdb=" CA ASN H 76 " ideal model delta sigma weight residual 122.08 128.13 -6.05 1.47e+00 4.63e-01 1.69e+01 angle pdb=" CA LEU H 31 " pdb=" CB LEU H 31 " pdb=" CG LEU H 31 " ideal model delta sigma weight residual 116.30 125.41 -9.11 3.50e+00 8.16e-02 6.77e+00 angle pdb=" C PHE A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.71e+00 angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 120.97 126.69 -5.72 2.84e+00 1.24e-01 4.06e+00 angle pdb=" C SER A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 122.40 125.31 -2.91 1.45e+00 4.76e-01 4.04e+00 ... (remaining 3410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 1317 17.44 - 34.87: 124 34.87 - 52.31: 19 52.31 - 69.75: 2 69.75 - 87.19: 2 Dihedral angle restraints: 1464 sinusoidal: 565 harmonic: 899 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 1.19 -87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -117.86 31.86 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA GLU H 103 " pdb=" C GLU H 103 " pdb=" N LEU H 104 " pdb=" CA LEU H 104 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 220 0.034 - 0.068: 92 0.068 - 0.102: 31 0.102 - 0.135: 16 0.135 - 0.169: 4 Chirality restraints: 363 Sorted by residual: chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA ASN H 76 " pdb=" N ASN H 76 " pdb=" C ASN H 76 " pdb=" CB ASN H 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 360 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 463 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.11e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 384 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.014 5.00e-02 4.00e+02 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 654 2.79 - 3.32: 2058 3.32 - 3.85: 4163 3.85 - 4.37: 4467 4.37 - 4.90: 7751 Nonbonded interactions: 19093 Sorted by model distance: nonbonded pdb=" O GLU H 1 " pdb=" OG SER H 25 " model vdw 2.267 3.040 nonbonded pdb=" O GLY H 10 " pdb=" OG1 THR H 117 " model vdw 2.311 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.318 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.364 3.040 nonbonded pdb=" OG SER H 17 " pdb=" OD1 ASN H 83 " model vdw 2.368 3.040 ... (remaining 19088 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2513 Z= 0.156 Angle : 0.670 9.107 3415 Z= 0.348 Chirality : 0.048 0.169 363 Planarity : 0.004 0.031 444 Dihedral : 13.499 77.692 883 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.45), residues: 310 helix: -4.21 (0.52), residues: 34 sheet: -0.20 (0.60), residues: 74 loop : -1.37 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 347 TYR 0.010 0.001 TYR A 453 ARG 0.005 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.8907 (tp) cc_final: 0.8552 (tp) REVERT: H 34 MET cc_start: 0.7425 (tmm) cc_final: 0.6735 (tmm) REVERT: H 36 TRP cc_start: 0.7575 (m100) cc_final: 0.6672 (t-100) REVERT: H 78 LEU cc_start: 0.7812 (tt) cc_final: 0.7470 (tt) REVERT: A 340 GLU cc_start: 0.9163 (pt0) cc_final: 0.8881 (pm20) REVERT: A 452 LEU cc_start: 0.9286 (mm) cc_final: 0.8854 (mm) REVERT: A 454 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8809 (mtt-85) REVERT: A 465 GLU cc_start: 0.9101 (tt0) cc_final: 0.8689 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2383 time to fit residues: 22.3827 Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 2513 Z= 0.285 Angle : 0.673 6.617 3415 Z= 0.356 Chirality : 0.045 0.145 363 Planarity : 0.004 0.034 444 Dihedral : 5.049 19.919 348 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.38 % Allowed : 7.17 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.45), residues: 310 helix: -4.12 (0.46), residues: 39 sheet: -1.14 (0.49), residues: 98 loop : -0.97 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.003 0.002 HIS A 519 PHE 0.015 0.002 PHE A 347 TYR 0.015 0.001 TYR H 93 ARG 0.003 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7262 (tmm) cc_final: 0.6713 (tmm) REVERT: H 78 LEU cc_start: 0.8044 (tt) cc_final: 0.7710 (tt) REVERT: H 107 PHE cc_start: 0.8092 (m-10) cc_final: 0.6949 (m-80) REVERT: A 454 ARG cc_start: 0.9255 (ttm-80) cc_final: 0.8777 (mmt180) REVERT: A 461 LEU cc_start: 0.8591 (pt) cc_final: 0.8034 (pp) REVERT: A 465 GLU cc_start: 0.9003 (tt0) cc_final: 0.7930 (tm-30) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.2142 time to fit residues: 10.7472 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN H 76 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2513 Z= 0.241 Angle : 0.615 5.082 3415 Z= 0.319 Chirality : 0.043 0.123 363 Planarity : 0.004 0.037 444 Dihedral : 5.056 23.451 348 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.38 % Allowed : 6.42 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.46), residues: 310 helix: -3.93 (0.56), residues: 33 sheet: -0.80 (0.55), residues: 88 loop : -1.05 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.003 0.002 HIS A 519 PHE 0.014 0.002 PHE A 338 TYR 0.010 0.001 TYR H 94 ARG 0.003 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 PHE cc_start: 0.8062 (m-10) cc_final: 0.7600 (m-80) REVERT: H 110 TRP cc_start: 0.7343 (m-90) cc_final: 0.7011 (m-90) REVERT: A 402 ILE cc_start: 0.9403 (tp) cc_final: 0.8940 (tp) REVERT: A 454 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.8977 (mmt90) REVERT: A 461 LEU cc_start: 0.8680 (pt) cc_final: 0.8239 (pp) REVERT: A 465 GLU cc_start: 0.9058 (tt0) cc_final: 0.8098 (tm-30) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.2131 time to fit residues: 11.8648 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2513 Z= 0.194 Angle : 0.611 6.514 3415 Z= 0.309 Chirality : 0.043 0.128 363 Planarity : 0.004 0.037 444 Dihedral : 4.894 22.834 348 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.46), residues: 310 helix: -3.51 (0.65), residues: 33 sheet: -0.00 (0.57), residues: 81 loop : -1.11 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE A 338 TYR 0.007 0.001 TYR H 93 ARG 0.003 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 PHE cc_start: 0.7897 (m-10) cc_final: 0.6818 (m-80) REVERT: A 454 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.8984 (mmt90) REVERT: A 461 LEU cc_start: 0.8718 (pt) cc_final: 0.8182 (pp) REVERT: A 465 GLU cc_start: 0.9030 (tt0) cc_final: 0.8045 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2252 time to fit residues: 11.0645 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.0050 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2513 Z= 0.209 Angle : 0.647 10.192 3415 Z= 0.329 Chirality : 0.046 0.260 363 Planarity : 0.003 0.036 444 Dihedral : 4.956 21.744 348 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.38 % Allowed : 4.15 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.46), residues: 310 helix: -3.42 (0.71), residues: 33 sheet: 0.21 (0.60), residues: 73 loop : -1.23 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.001 PHE A 392 TYR 0.008 0.001 TYR H 93 ARG 0.005 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 TRP cc_start: 0.7248 (m-90) cc_final: 0.6930 (m-90) REVERT: H 112 GLN cc_start: 0.7680 (mm-40) cc_final: 0.6731 (pm20) REVERT: A 454 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.8957 (mmt90) REVERT: A 461 LEU cc_start: 0.8737 (pt) cc_final: 0.8216 (pp) REVERT: A 465 GLU cc_start: 0.9035 (tt0) cc_final: 0.8099 (tm-30) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1788 time to fit residues: 8.8327 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 0.0020 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2513 Z= 0.234 Angle : 0.689 10.733 3415 Z= 0.352 Chirality : 0.045 0.175 363 Planarity : 0.003 0.036 444 Dihedral : 5.571 27.056 348 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.46), residues: 310 helix: -3.20 (0.73), residues: 33 sheet: 0.51 (0.62), residues: 72 loop : -1.46 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.002 0.002 HIS A 519 PHE 0.020 0.002 PHE A 429 TYR 0.010 0.002 TYR A 421 ARG 0.004 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 PHE cc_start: 0.7757 (m-80) cc_final: 0.7503 (m-80) REVERT: A 454 ARG cc_start: 0.9280 (ttm-80) cc_final: 0.8858 (mmt90) REVERT: A 461 LEU cc_start: 0.8594 (pt) cc_final: 0.8007 (pp) REVERT: A 465 GLU cc_start: 0.8936 (tt0) cc_final: 0.7968 (tm-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1996 time to fit residues: 8.2649 Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2513 Z= 0.147 Angle : 0.636 9.219 3415 Z= 0.315 Chirality : 0.045 0.168 363 Planarity : 0.003 0.033 444 Dihedral : 4.809 24.788 348 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -1.71 (0.45), residues: 310 helix: -3.13 (0.73), residues: 33 sheet: 0.58 (0.61), residues: 72 loop : -1.51 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.017 0.001 PHE A 429 TYR 0.017 0.001 TYR H 33 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7912 (mpp-170) cc_final: 0.7533 (mpp-170) REVERT: H 112 GLN cc_start: 0.7678 (mm-40) cc_final: 0.6787 (pm20) REVERT: A 402 ILE cc_start: 0.9363 (tp) cc_final: 0.9021 (tp) REVERT: A 454 ARG cc_start: 0.9279 (ttm-80) cc_final: 0.8898 (mmt90) REVERT: A 461 LEU cc_start: 0.8578 (pt) cc_final: 0.7884 (pp) REVERT: A 465 GLU cc_start: 0.9034 (tt0) cc_final: 0.8018 (tm-30) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1863 time to fit residues: 10.1741 Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.0670 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 18 optimal weight: 7.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2513 Z= 0.136 Angle : 0.632 8.523 3415 Z= 0.315 Chirality : 0.045 0.173 363 Planarity : 0.003 0.030 444 Dihedral : 4.581 25.753 348 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.45), residues: 310 helix: -3.32 (0.65), residues: 33 sheet: 0.59 (0.60), residues: 72 loop : -1.46 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.019 0.001 PHE A 429 TYR 0.010 0.001 TYR H 93 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7828 (mpp-170) cc_final: 0.7428 (mpp-170) REVERT: H 112 GLN cc_start: 0.7556 (mm-40) cc_final: 0.6479 (pm20) REVERT: A 392 PHE cc_start: 0.8206 (m-80) cc_final: 0.7545 (m-80) REVERT: A 454 ARG cc_start: 0.9256 (ttm-80) cc_final: 0.8858 (mmt90) REVERT: A 461 LEU cc_start: 0.8672 (pt) cc_final: 0.8002 (pp) REVERT: A 465 GLU cc_start: 0.9054 (tt0) cc_final: 0.8040 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1920 time to fit residues: 9.5483 Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2513 Z= 0.170 Angle : 0.638 8.025 3415 Z= 0.321 Chirality : 0.045 0.165 363 Planarity : 0.003 0.027 444 Dihedral : 4.799 25.802 348 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.46), residues: 310 helix: -3.26 (0.65), residues: 33 sheet: 0.66 (0.61), residues: 72 loop : -1.40 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.001 PHE A 429 TYR 0.010 0.001 TYR H 33 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7934 (mpp-170) cc_final: 0.7446 (mpp-170) REVERT: A 392 PHE cc_start: 0.8457 (m-80) cc_final: 0.7668 (m-80) REVERT: A 454 ARG cc_start: 0.9234 (ttm-80) cc_final: 0.8868 (mmt90) REVERT: A 461 LEU cc_start: 0.8808 (pt) cc_final: 0.8163 (pp) REVERT: A 465 GLU cc_start: 0.9036 (tt0) cc_final: 0.8071 (tm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2085 time to fit residues: 9.6780 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2513 Z= 0.137 Angle : 0.623 7.454 3415 Z= 0.308 Chirality : 0.043 0.173 363 Planarity : 0.003 0.027 444 Dihedral : 4.593 24.713 348 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.46), residues: 310 helix: -3.05 (0.70), residues: 33 sheet: 0.74 (0.62), residues: 72 loop : -1.35 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.001 PHE A 429 TYR 0.007 0.001 TYR A 351 ARG 0.002 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7808 (mpp-170) cc_final: 0.7385 (mpp-170) REVERT: H 101 PHE cc_start: 0.8513 (t80) cc_final: 0.8296 (t80) REVERT: H 107 PHE cc_start: 0.7246 (m-10) cc_final: 0.6711 (m-80) REVERT: A 392 PHE cc_start: 0.8402 (m-80) cc_final: 0.7630 (m-80) REVERT: A 454 ARG cc_start: 0.9247 (ttm-80) cc_final: 0.8849 (mmt90) REVERT: A 461 LEU cc_start: 0.8883 (pt) cc_final: 0.8215 (pp) REVERT: A 465 GLU cc_start: 0.9080 (tt0) cc_final: 0.8078 (tm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2022 time to fit residues: 9.3734 Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.0170 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.077465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063158 restraints weight = 16803.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.065804 restraints weight = 15057.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.066849 restraints weight = 9155.406| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2513 Z= 0.125 Angle : 0.603 7.115 3415 Z= 0.298 Chirality : 0.043 0.172 363 Planarity : 0.003 0.025 444 Dihedral : 4.407 24.342 348 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.46), residues: 310 helix: -2.86 (0.76), residues: 31 sheet: 0.91 (0.62), residues: 72 loop : -1.31 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE A 429 TYR 0.012 0.001 TYR H 33 ARG 0.002 0.000 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.51 seconds wall clock time: 20 minutes 50.93 seconds (1250.93 seconds total)