Starting phenix.real_space_refine on Wed Oct 9 23:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iwq_60959/10_2024/9iwq_60959.cif" } resolution = 2.08 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= 0.012 sd= 0.114 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 S 2 5.16 5 C 1720 2.51 5 N 518 2.21 5 O 613 1.98 5 H 2830 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 5683 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 5683 Classifications: {'peptide': 387} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 383} Chain breaks: 1 Time building chain proxies: 3.38, per 1000 atoms: 0.59 Number of scatterers: 5683 At special positions: 0 Unit cell: (88.74, 66.12, 158.34, 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 2 16.00 O 613 8.00 N 518 7.00 C 1720 6.00 H 2830 1.00 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: 1.44 Conformation dependent library (CDL) restraints added in 417.3 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 54.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.846A pdb=" N ASN A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 99 removed outlier: 3.737A pdb=" N GLU A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.558A pdb=" N GLU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 406 through 455 removed outlier: 3.554A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 485 removed outlier: 3.523A pdb=" N SER A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 removed outlier: 4.323A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 146 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.754A pdb=" N GLY A 322 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR A 311 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 320 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 14.746A pdb=" N GLY A 321 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLN A 336 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 323 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 364 201 hydrogen bonds defined for protein. 579 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: 1.87 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 906 1.03 - 1.23: 2096 1.23 - 1.42: 1086 1.42 - 1.62: 1604 1.62 - 1.81: 4 Bond restraints: 5696 Sorted by residual: bond pdb=" CA ASN A 406 " pdb=" CB ASN A 406 " ideal model delta sigma weight residual 1.522 1.461 0.061 7.00e-03 2.04e+04 7.63e+01 bond pdb=" N THR A 6 " pdb=" H THR A 6 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ASN A 5 " pdb=" H ASN A 5 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N GLY A 148 " pdb=" CA GLY A 148 " ideal model delta sigma weight residual 1.444 1.370 0.073 9.10e-03 1.21e+04 6.51e+01 bond pdb=" N GLU A 153 " pdb=" H GLU A 153 " ideal model delta sigma weight residual 0.860 1.013 -0.153 2.00e-02 2.50e+03 5.82e+01 ... (remaining 5691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 7631 2.17 - 4.34: 1833 4.34 - 6.52: 569 6.52 - 8.69: 211 8.69 - 10.86: 17 Bond angle restraints: 10261 Sorted by residual: angle pdb=" CA ASP A 419 " pdb=" CB ASP A 419 " pdb=" CG ASP A 419 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.00e+00 1.00e+00 5.91e+01 angle pdb=" CA ASN A 5 " pdb=" CB ASN A 5 " pdb=" CG ASN A 5 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA ASN A 16 " pdb=" CB ASN A 16 " pdb=" CG ASN A 16 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " pdb=" CG ASN A 15 " ideal model delta sigma weight residual 112.60 119.50 -6.90 1.00e+00 1.00e+00 4.75e+01 angle pdb=" CA ASN A 406 " pdb=" CB ASN A 406 " pdb=" CG ASN A 406 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.00e+00 1.00e+00 4.70e+01 ... (remaining 10256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2480 17.80 - 35.61: 109 35.61 - 53.41: 29 53.41 - 71.21: 42 71.21 - 89.01: 5 Dihedral angle restraints: 2665 sinusoidal: 1502 harmonic: 1163 Sorted by residual: dihedral pdb=" N ASN A 5 " pdb=" C ASN A 5 " pdb=" CA ASN A 5 " pdb=" CB ASN A 5 " ideal model delta harmonic sigma weight residual 122.80 134.42 -11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N LYS A 19 " pdb=" C LYS A 19 " pdb=" CA LYS A 19 " pdb=" CB LYS A 19 " ideal model delta harmonic sigma weight residual 122.80 133.77 -10.97 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C GLU A 153 " pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" CB GLU A 153 " ideal model delta harmonic sigma weight residual -122.60 -133.38 10.78 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 2662 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.143: 385 0.143 - 0.285: 20 0.285 - 0.428: 6 0.428 - 0.570: 55 0.570 - 0.713: 13 Chirality restraints: 479 Sorted by residual: chirality pdb=" CG LEU A 11 " pdb=" CB LEU A 11 " pdb=" CD1 LEU A 11 " pdb=" CD2 LEU A 11 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CG LEU A 12 " pdb=" CB LEU A 12 " pdb=" CD1 LEU A 12 " pdb=" CD2 LEU A 12 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL A 147 " pdb=" CA VAL A 147 " pdb=" CG1 VAL A 147 " pdb=" CG2 VAL A 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.41e+00 ... (remaining 476 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.154 2.00e-02 2.50e+03 6.17e-02 1.14e+02 pdb=" CG PHE A 131 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 131 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 131 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 131 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 131 " 0.011 2.00e-02 2.50e+03 pdb=" HZ PHE A 131 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 175 " -0.038 2.00e-02 2.50e+03 5.19e-02 4.03e+01 pdb=" CD GLN A 175 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN A 175 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 175 " 0.094 2.00e-02 2.50e+03 pdb="HE21 GLN A 175 " -0.013 2.00e-02 2.50e+03 pdb="HE22 GLN A 175 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 388 " 0.078 2.00e-02 2.50e+03 4.17e-02 3.91e+01 pdb=" CG HIS A 388 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A 388 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS A 388 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 388 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS A 388 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 HIS A 388 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS A 388 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS A 388 " 0.059 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 433 2.24 - 2.83: 11360 2.83 - 3.42: 15300 3.42 - 4.01: 19425 4.01 - 4.60: 28464 Nonbonded interactions: 74982 Sorted by model distance: nonbonded pdb=" H ARG A 36 " pdb=" O GLU A 454 " model vdw 1.649 2.450 nonbonded pdb=" HG SER A 104 " pdb=" OD2 ASP A 107 " model vdw 1.656 2.450 nonbonded pdb=" HG SER A 126 " pdb=" O ILE A 162 " model vdw 1.705 2.450 nonbonded pdb=" O VAL A 125 " pdb=" HG1 THR A 129 " model vdw 1.706 2.450 nonbonded pdb=" O GLN A 175 " pdb=" HG1 THR A 403 " model vdw 1.721 2.450 ... (remaining 74977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 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 : 0.022 0.138 2866 Z= 1.464 Angle : 2.143 10.859 3887 Z= 1.488 Chirality : 0.215 0.713 479 Planarity : 0.010 0.072 522 Dihedral : 12.563 89.014 1046 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 5.83 % 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: 1.04 (0.40), residues: 383 helix: 1.30 (0.32), residues: 204 sheet: -0.34 (0.51), residues: 67 loop : 0.49 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 388 PHE 0.104 0.019 PHE A 131 TYR 0.071 0.016 TYR A 332 ARG 0.004 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.388 Fit side-chains REVERT: A 130 GLN cc_start: 0.8734 (pt0) cc_final: 0.8487 (pp30) REVERT: A 484 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8546 (mm-40) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 2.7821 time to fit residues: 82.8401 Evaluate side-chains 24 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.9130 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2866 Z= 0.231 Angle : 0.523 3.881 3887 Z= 0.313 Chirality : 0.039 0.135 479 Planarity : 0.004 0.039 522 Dihedral : 4.888 18.352 407 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 2.39 (0.41), residues: 383 helix: 2.87 (0.33), residues: 198 sheet: -0.35 (0.57), residues: 56 loop : 0.51 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 388 PHE 0.031 0.005 PHE A 131 TYR 0.011 0.002 TYR A 458 ARG 0.004 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.468 Fit side-chains REVERT: A 130 GLN cc_start: 0.8741 (pt0) cc_final: 0.8438 (pp30) REVERT: A 484 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8293 (mm-40) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 2.8588 time to fit residues: 73.4674 Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2866 Z= 0.141 Angle : 0.399 3.199 3887 Z= 0.239 Chirality : 0.035 0.137 479 Planarity : 0.003 0.037 522 Dihedral : 4.159 16.535 407 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.32 % Allowed : 3.87 % Favored : 95.81 % 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: 3.09 (0.44), residues: 383 helix: 3.70 (0.35), residues: 198 sheet: -1.02 (0.62), residues: 45 loop : 0.72 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 388 PHE 0.016 0.002 PHE A 131 TYR 0.007 0.001 TYR A 331 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.454 Fit side-chains REVERT: A 131 PHE cc_start: 0.8117 (t80) cc_final: 0.7909 (t80) REVERT: A 484 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8017 (mm-40) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 2.8809 time to fit residues: 71.1653 Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2866 Z= 0.184 Angle : 0.437 3.516 3887 Z= 0.258 Chirality : 0.036 0.135 479 Planarity : 0.003 0.036 522 Dihedral : 4.226 17.024 407 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.29 % Allowed : 5.16 % Favored : 93.55 % 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: 3.18 (0.44), residues: 383 helix: 3.72 (0.35), residues: 198 sheet: -0.57 (0.54), residues: 59 loop : 0.85 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 388 PHE 0.025 0.003 PHE A 131 TYR 0.008 0.001 TYR A 458 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.499 Fit side-chains REVERT: A 484 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8073 (mm-40) outliers start: 4 outliers final: 0 residues processed: 27 average time/residue: 2.6946 time to fit residues: 74.8849 Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2866 Z= 0.214 Angle : 0.454 4.034 3887 Z= 0.269 Chirality : 0.037 0.135 479 Planarity : 0.003 0.038 522 Dihedral : 4.335 22.980 407 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.61 % Allowed : 5.16 % Favored : 93.23 % 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: 3.03 (0.43), residues: 383 helix: 3.55 (0.34), residues: 198 sheet: -0.31 (0.56), residues: 57 loop : 0.66 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 388 PHE 0.026 0.003 PHE A 131 TYR 0.008 0.001 TYR A 458 ARG 0.004 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.451 Fit side-chains REVERT: A 2 GLN cc_start: 0.6048 (mt0) cc_final: 0.5379 (mm110) REVERT: A 484 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8231 (mm-40) outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 2.8707 time to fit residues: 79.6974 Evaluate side-chains 27 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2866 Z= 0.171 Angle : 0.416 4.223 3887 Z= 0.245 Chirality : 0.036 0.133 479 Planarity : 0.003 0.037 522 Dihedral : 4.203 24.090 407 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.29 % Allowed : 5.48 % Favored : 93.23 % 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: 3.24 (0.44), residues: 383 helix: 3.73 (0.35), residues: 198 sheet: -0.26 (0.56), residues: 57 loop : 0.77 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 388 PHE 0.025 0.003 PHE A 131 TYR 0.007 0.001 TYR A 458 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.429 Fit side-chains REVERT: A 2 GLN cc_start: 0.6008 (mt0) cc_final: 0.5390 (mm110) REVERT: A 484 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8073 (mm-40) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 2.6301 time to fit residues: 73.0519 Evaluate side-chains 27 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2866 Z= 0.215 Angle : 0.455 4.700 3887 Z= 0.266 Chirality : 0.037 0.134 479 Planarity : 0.003 0.038 522 Dihedral : 4.314 26.734 407 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.61 % Allowed : 5.16 % Favored : 93.23 % 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: 3.08 (0.43), residues: 383 helix: 3.58 (0.34), residues: 198 sheet: -0.32 (0.56), residues: 59 loop : 0.76 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 388 PHE 0.031 0.004 PHE A 131 TYR 0.008 0.001 TYR A 458 ARG 0.004 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 31 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.443 Fit side-chains REVERT: A 2 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.5457 (mm110) REVERT: A 484 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8161 (mm-40) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 2.6822 time to fit residues: 77.2052 Evaluate side-chains 29 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 488 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 40.0000 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 130 GLN A 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2866 Z= 0.178 Angle : 0.427 5.203 3887 Z= 0.249 Chirality : 0.036 0.133 479 Planarity : 0.003 0.039 522 Dihedral : 4.203 26.058 407 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.29 % Allowed : 5.48 % Favored : 93.23 % 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: 3.23 (0.44), residues: 383 helix: 3.72 (0.35), residues: 198 sheet: -0.15 (0.58), residues: 57 loop : 0.72 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 388 PHE 0.028 0.003 PHE A 131 TYR 0.007 0.001 TYR A 458 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 31 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.441 Fit side-chains REVERT: A 2 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5417 (mm110) REVERT: A 484 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8091 (mm-40) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 2.7199 time to fit residues: 78.2856 Evaluate side-chains 29 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2866 Z= 0.174 Angle : 0.425 5.788 3887 Z= 0.246 Chirality : 0.036 0.133 479 Planarity : 0.003 0.039 522 Dihedral : 4.134 25.209 407 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.29 % Allowed : 5.48 % Favored : 93.23 % 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: 3.25 (0.44), residues: 383 helix: 3.76 (0.35), residues: 198 sheet: -0.19 (0.57), residues: 57 loop : 0.69 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 388 PHE 0.027 0.003 PHE A 131 TYR 0.007 0.001 TYR A 458 ARG 0.002 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.481 Fit side-chains REVERT: A 2 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.5486 (mm110) REVERT: A 484 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8034 (mm-40) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 2.8314 time to fit residues: 78.6280 Evaluate side-chains 28 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2866 Z= 0.122 Angle : 0.375 6.195 3887 Z= 0.215 Chirality : 0.035 0.133 479 Planarity : 0.002 0.037 522 Dihedral : 3.745 19.634 407 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.65 % Allowed : 6.13 % Favored : 93.23 % 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: 3.61 (0.45), residues: 383 helix: 4.11 (0.35), residues: 198 sheet: -0.20 (0.57), residues: 57 loop : 0.86 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 388 PHE 0.012 0.001 PHE A 131 TYR 0.005 0.001 TYR A 178 ARG 0.002 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 26 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.487 Fit side-chains REVERT: A 484 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7801 (mm-40) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 2.8625 time to fit residues: 73.6616 Evaluate side-chains 25 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.0770 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110907 restraints weight = 7180.464| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.17 r_work: 0.3181 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3009 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2866 Z= 0.169 Angle : 0.414 6.111 3887 Z= 0.237 Chirality : 0.036 0.131 479 Planarity : 0.003 0.036 522 Dihedral : 3.947 21.504 407 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.55 % 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: 3.45 (0.44), residues: 383 helix: 3.96 (0.35), residues: 198 sheet: -0.20 (0.57), residues: 57 loop : 0.78 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 388 PHE 0.012 0.002 PHE A 131 TYR 0.007 0.001 TYR A 458 ARG 0.002 0.000 ARG A 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.64 seconds wall clock time: 49 minutes 18.12 seconds (2958.12 seconds total)