Starting phenix.real_space_refine on Sun Mar 10 16:59:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcr_38252/03_2024/8xcr_38252_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 21} Link IDs: {None: 22} Time building chain proxies: 2.39, per 1000 atoms: 0.71 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 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 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 758.7 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.616A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.690A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.623A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.848A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.180A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.807A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 161 hydrogen bonds defined for protein. 468 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: 1.03 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1056 1.34 - 1.45: 438 1.45 - 1.57: 1889 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C3N NAP A 500 " pdb=" C4N NAP A 500 " ideal model delta sigma weight residual 1.390 1.511 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C TRP A 364 " pdb=" N THR A 365 " ideal model delta sigma weight residual 1.328 1.413 -0.085 1.62e-02 3.81e+03 2.77e+01 bond pdb=" C4A NAP A 500 " pdb=" C5A NAP A 500 " ideal model delta sigma weight residual 1.385 1.469 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5A NAP A 500 " pdb=" C6A NAP A 500 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.45: 147 107.45 - 114.63: 2014 114.63 - 121.81: 1731 121.81 - 128.99: 714 128.99 - 136.17: 32 Bond angle restraints: 4638 Sorted by residual: angle pdb=" N GLN A 60 " pdb=" CA GLN A 60 " pdb=" C GLN A 60 " ideal model delta sigma weight residual 109.07 101.44 7.63 1.61e+00 3.86e-01 2.25e+01 angle pdb=" N GLU A 325 " pdb=" CA GLU A 325 " pdb=" C GLU A 325 " ideal model delta sigma weight residual 111.07 106.75 4.32 1.07e+00 8.73e-01 1.63e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 118.97 122.36 -3.39 1.04e+00 9.25e-01 1.06e+01 angle pdb=" N VAL A 300 " pdb=" CA VAL A 300 " pdb=" C VAL A 300 " ideal model delta sigma weight residual 113.42 109.81 3.61 1.17e+00 7.31e-01 9.53e+00 angle pdb=" C2A NAP A 500 " pdb=" N3A NAP A 500 " pdb=" C4A NAP A 500 " ideal model delta sigma weight residual 111.82 120.84 -9.02 3.00e+00 1.11e-01 9.03e+00 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1808 17.91 - 35.82: 184 35.82 - 53.73: 54 53.73 - 71.64: 29 71.64 - 89.55: 7 Dihedral angle restraints: 2082 sinusoidal: 885 harmonic: 1197 Sorted by residual: dihedral pdb=" CA ASP A 340 " pdb=" CB ASP A 340 " pdb=" CG ASP A 340 " pdb=" OD1 ASP A 340 " ideal model delta sinusoidal sigma weight residual -30.00 -86.78 56.78 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU A 371 " pdb=" CG GLU A 371 " pdb=" CD GLU A 371 " pdb=" OE1 GLU A 371 " ideal model delta sinusoidal sigma weight residual 0.00 -88.93 88.93 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 2079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 385 0.047 - 0.094: 79 0.094 - 0.141: 35 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA GLN A 60 " pdb=" N GLN A 60 " pdb=" C GLN A 60 " pdb=" CB GLN A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1B NAP A 500 " pdb=" C2B NAP A 500 " pdb=" N9A NAP A 500 " pdb=" O4B NAP A 500 " both_signs ideal model delta sigma weight residual False 2.31 2.50 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 502 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ILE A 297 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 298 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 18 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C ALA A 18 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 18 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 19 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 150 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.023 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 1332 2.90 - 3.40: 3333 3.40 - 3.90: 6093 3.90 - 4.40: 7140 4.40 - 4.90: 11479 Nonbonded interactions: 29377 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.405 2.440 nonbonded pdb=" N ASN A 222 " pdb=" O2A NAP A 500 " model vdw 2.455 2.520 nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 602 " model vdw 2.481 2.440 nonbonded pdb=" OD1 ASP A 145 " pdb=" O GGL A 501 " model vdw 2.486 3.040 nonbonded pdb=" O1N NAP A 500 " pdb=" O HOH A 603 " model vdw 2.494 2.440 ... (remaining 29372 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: 0.660 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: 3.430 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.800 Find NCS groups from input model: 0.090 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 : 0.006 0.128 3415 Z= 0.407 Angle : 0.766 9.015 4638 Z= 0.454 Chirality : 0.047 0.235 505 Planarity : 0.004 0.041 589 Dihedral : 18.073 89.554 1318 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.45 % Allowed : 3.52 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.43), residues: 416 helix: 0.90 (0.36), residues: 210 sheet: 0.60 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.410 Fit side-chains REVERT: A 16 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7941 (ttm170) REVERT: A 327 ASP cc_start: 0.7280 (m-30) cc_final: 0.6822 (m-30) outliers start: 22 outliers final: 7 residues processed: 81 average time/residue: 1.4198 time to fit residues: 117.8399 Evaluate side-chains 59 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.193 Angle : 0.475 5.989 4638 Z= 0.247 Chirality : 0.043 0.129 505 Planarity : 0.004 0.044 589 Dihedral : 12.891 83.473 543 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.47 % Allowed : 11.14 % Favored : 87.39 % 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: 1.29 (0.43), residues: 416 helix: 1.83 (0.37), residues: 211 sheet: 0.38 (0.70), residues: 61 loop : -0.34 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.006 0.002 HIS A 61 PHE 0.014 0.002 PHE A 341 TYR 0.010 0.002 TYR A 147 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.410 Fit side-chains REVERT: A 21 MET cc_start: 0.8496 (ptt) cc_final: 0.8248 (ptt) REVERT: A 267 HIS cc_start: 0.8372 (m90) cc_final: 0.8083 (m-70) REVERT: A 271 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8364 (tttm) outliers start: 5 outliers final: 1 residues processed: 53 average time/residue: 1.6500 time to fit residues: 89.4909 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.8768 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3415 Z= 0.219 Angle : 0.469 4.219 4638 Z= 0.245 Chirality : 0.043 0.129 505 Planarity : 0.004 0.049 589 Dihedral : 11.584 87.947 527 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.05 % Allowed : 11.14 % Favored : 86.80 % 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: 1.36 (0.43), residues: 416 helix: 1.90 (0.37), residues: 211 sheet: 0.35 (0.70), residues: 61 loop : -0.29 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.374 Fit side-chains REVERT: A 21 MET cc_start: 0.8578 (ptt) cc_final: 0.8282 (ptt) REVERT: A 191 THR cc_start: 0.8478 (t) cc_final: 0.8054 (m) REVERT: A 267 HIS cc_start: 0.8414 (m90) cc_final: 0.8192 (m-70) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 1.7026 time to fit residues: 90.5998 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.0030 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3415 Z= 0.153 Angle : 0.435 4.069 4638 Z= 0.226 Chirality : 0.042 0.129 505 Planarity : 0.004 0.048 589 Dihedral : 11.041 79.900 527 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.17 % Allowed : 12.90 % Favored : 85.92 % 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: 1.47 (0.43), residues: 416 helix: 2.02 (0.36), residues: 210 sheet: 0.37 (0.70), residues: 61 loop : -0.24 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.426 Fit side-chains REVERT: A 3 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6027 (mm-30) REVERT: A 21 MET cc_start: 0.8508 (ptt) cc_final: 0.8178 (ptt) REVERT: A 267 HIS cc_start: 0.8369 (m90) cc_final: 0.8162 (m-70) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 1.8044 time to fit residues: 86.7934 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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: 0.8777 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3415 Z= 0.233 Angle : 0.472 4.437 4638 Z= 0.246 Chirality : 0.044 0.130 505 Planarity : 0.004 0.050 589 Dihedral : 11.041 80.433 527 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.47 % Allowed : 14.08 % Favored : 84.46 % 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: 1.44 (0.43), residues: 416 helix: 2.01 (0.36), residues: 209 sheet: 0.38 (0.70), residues: 61 loop : -0.28 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.423 Fit side-chains REVERT: A 3 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5974 (mm-30) REVERT: A 21 MET cc_start: 0.8597 (ptt) cc_final: 0.8309 (ptt) REVERT: A 267 HIS cc_start: 0.8379 (m90) cc_final: 0.8151 (m90) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 1.7308 time to fit residues: 84.9500 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3415 Z= 0.122 Angle : 0.411 4.014 4638 Z= 0.214 Chirality : 0.041 0.129 505 Planarity : 0.004 0.047 589 Dihedral : 10.271 69.788 527 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.76 % Allowed : 13.20 % Favored : 85.04 % 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 (0.44), residues: 416 helix: 2.10 (0.36), residues: 210 sheet: 0.43 (0.71), residues: 61 loop : -0.11 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 400 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.388 Fit side-chains REVERT: A 21 MET cc_start: 0.8468 (ptt) cc_final: 0.8209 (ptt) REVERT: A 267 HIS cc_start: 0.8366 (m90) cc_final: 0.8163 (m-70) REVERT: A 271 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8412 (tttm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 1.7804 time to fit residues: 89.1596 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3415 Z= 0.254 Angle : 0.481 4.973 4638 Z= 0.251 Chirality : 0.044 0.130 505 Planarity : 0.005 0.050 589 Dihedral : 10.664 74.609 527 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 14.08 % Favored : 84.46 % 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: 1.46 (0.44), residues: 416 helix: 1.98 (0.36), residues: 209 sheet: 0.45 (0.71), residues: 61 loop : -0.22 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.012 0.002 TYR A 363 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.410 Fit side-chains REVERT: A 21 MET cc_start: 0.8607 (ptt) cc_final: 0.8316 (ptt) REVERT: A 267 HIS cc_start: 0.8398 (m90) cc_final: 0.8179 (m90) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 1.8044 time to fit residues: 86.7681 Evaluate side-chains 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3415 Z= 0.126 Angle : 0.416 4.972 4638 Z= 0.216 Chirality : 0.041 0.129 505 Planarity : 0.004 0.048 589 Dihedral : 9.953 65.554 527 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.17 % Allowed : 14.37 % Favored : 84.46 % 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: 1.64 (0.44), residues: 416 helix: 2.11 (0.36), residues: 210 sheet: 0.46 (0.71), residues: 61 loop : -0.09 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.001 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.395 Fit side-chains REVERT: A 21 MET cc_start: 0.8473 (ptt) cc_final: 0.8241 (ptt) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 1.7901 time to fit residues: 86.0736 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3415 Z= 0.193 Angle : 0.454 6.213 4638 Z= 0.236 Chirality : 0.043 0.129 505 Planarity : 0.004 0.049 589 Dihedral : 10.042 65.767 527 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 15.25 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.44), residues: 416 helix: 2.08 (0.36), residues: 209 sheet: 0.47 (0.71), residues: 61 loop : -0.16 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.401 Fit side-chains REVERT: A 21 MET cc_start: 0.8558 (ptt) cc_final: 0.8345 (ptt) REVERT: A 191 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.7940 (m) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 1.7819 time to fit residues: 83.8457 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3415 Z= 0.114 Angle : 0.408 6.420 4638 Z= 0.211 Chirality : 0.041 0.135 505 Planarity : 0.004 0.047 589 Dihedral : 9.303 59.311 527 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 14.96 % Favored : 84.16 % 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: 1.79 (0.44), residues: 416 helix: 2.22 (0.36), residues: 210 sheet: 0.48 (0.71), residues: 61 loop : 0.02 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.006 0.001 PHE A 341 TYR 0.007 0.001 TYR A 400 ARG 0.001 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.442 Fit side-chains REVERT: A 21 MET cc_start: 0.8413 (ptt) cc_final: 0.8118 (ptt) REVERT: A 191 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 388 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8301 (t70) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 1.6874 time to fit residues: 82.9902 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.097532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.074375 restraints weight = 4308.241| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 1.42 r_work: 0.2558 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3415 Z= 0.289 Angle : 0.505 7.387 4638 Z= 0.263 Chirality : 0.045 0.131 505 Planarity : 0.005 0.052 589 Dihedral : 10.206 66.310 527 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 15.25 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.44), residues: 416 helix: 2.01 (0.36), residues: 209 sheet: 0.40 (0.71), residues: 61 loop : -0.20 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 30 HIS 0.004 0.002 HIS A 388 PHE 0.019 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.52 seconds wall clock time: 35 minutes 23.16 seconds (2123.16 seconds total)