Starting phenix.real_space_refine on Wed Mar 5 16:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.map" model { file = "/net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt5_36633/03_2025/8jt5_36633.cif" } resolution = 3.06 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= -0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 1901 2.51 5 N 444 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2854 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2846 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.94 Number of scatterers: 2854 At special positions: 0 Unit cell: (56.58, 62.32, 71.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 482 8.00 N 444 7.00 C 1901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.651A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.745A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.476A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.855A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.698A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.659A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.753A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.894A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.638A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.666A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.546A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 549 1.33 - 1.45: 652 1.45 - 1.57: 1675 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2922 Sorted by residual: bond pdb=" CG HSM A 501 " pdb=" ND1 HSM A 501 " ideal model delta sigma weight residual 1.383 1.310 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N ILE A 43 " pdb=" CA ILE A 43 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.61e+00 bond pdb=" N VAL A 26 " pdb=" CA VAL A 26 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.56e+00 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.38e+00 bond pdb=" CD2 HSM A 501 " pdb=" NE2 HSM A 501 " ideal model delta sigma weight residual 1.376 1.318 0.058 2.00e-02 2.50e+03 8.37e+00 ... (remaining 2917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 3823 1.94 - 3.89: 129 3.89 - 5.83: 20 5.83 - 7.77: 4 7.77 - 9.72: 2 Bond angle restraints: 3978 Sorted by residual: angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.43 -2.60 6.10e-01 2.69e+00 1.82e+01 angle pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta sigma weight residual 110.50 113.11 -2.61 6.30e-01 2.52e+00 1.72e+01 angle pdb=" CA VAL A 410 " pdb=" C VAL A 410 " pdb=" O VAL A 410 " ideal model delta sigma weight residual 120.95 117.29 3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 120.95 117.48 3.47 1.04e+00 9.25e-01 1.12e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" O VAL A 41 " ideal model delta sigma weight residual 118.69 116.46 2.23 6.70e-01 2.23e+00 1.11e+01 ... (remaining 3973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1502 17.36 - 34.73: 158 34.73 - 52.09: 41 52.09 - 69.46: 6 69.46 - 86.82: 2 Dihedral angle restraints: 1709 sinusoidal: 623 harmonic: 1086 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -133.44 11.44 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 132.93 -9.53 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 378 0.054 - 0.108: 82 0.108 - 0.162: 14 0.162 - 0.216: 3 0.216 - 0.270: 2 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU A 23 " pdb=" N LEU A 23 " pdb=" C LEU A 23 " pdb=" CB LEU A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 476 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 166 " 0.003 2.00e-02 2.50e+03 1.74e-02 5.28e+00 pdb=" CG PHE A 166 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 166 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 166 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 166 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 166 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 166 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 161 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 473 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.023 5.00e-02 4.00e+02 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 695 2.79 - 3.32: 2917 3.32 - 3.85: 4803 3.85 - 4.37: 5552 4.37 - 4.90: 9741 Nonbonded interactions: 23708 Sorted by model distance: nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASN A 305 " pdb=" ND1 HSM A 501 " model vdw 2.337 3.120 nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.400 3.040 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.423 3.120 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.458 3.120 ... (remaining 23703 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.005 0.073 2922 Z= 0.332 Angle : 0.806 9.719 3978 Z= 0.489 Chirality : 0.050 0.270 479 Planarity : 0.006 0.052 489 Dihedral : 15.377 86.821 1017 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.11 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 23.67 % Favored : 74.67 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.42), residues: 380 helix: 1.63 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.89 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.033 0.002 PHE A 166 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.364 Fit side-chains REVERT: A 40 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8588 (t) REVERT: A 47 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6583 (t80) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.1385 time to fit residues: 10.0420 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132977 restraints weight = 3350.393| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.66 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2922 Z= 0.263 Angle : 0.691 9.852 3978 Z= 0.334 Chirality : 0.042 0.152 479 Planarity : 0.006 0.055 489 Dihedral : 5.702 55.727 412 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.00 % Allowed : 25.33 % Favored : 73.67 % 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: 1.92 (0.43), residues: 380 helix: 1.77 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.65 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.265 Fit side-chains REVERT: A 47 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6322 (t80) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.1116 time to fit residues: 8.0088 Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126731 restraints weight = 3364.883| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.76 r_work: 0.3179 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2922 Z= 0.277 Angle : 0.678 9.909 3978 Z= 0.326 Chirality : 0.043 0.150 479 Planarity : 0.006 0.055 489 Dihedral : 5.401 53.576 407 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 23.00 % Favored : 73.67 % 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: 1.88 (0.43), residues: 380 helix: 1.68 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.54 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.003 0.002 HIS A 353 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.001 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.314 Fit side-chains REVERT: A 35 MET cc_start: 0.7992 (mtt) cc_final: 0.7736 (mtt) REVERT: A 47 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6246 (t80) REVERT: A 433 TYR cc_start: 0.7753 (m-80) cc_final: 0.7363 (m-10) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.1384 time to fit residues: 9.9753 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 28 optimal weight: 0.0970 chunk 3 optimal weight: 0.0020 overall best weight: 0.2764 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.160824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139425 restraints weight = 3298.937| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.66 r_work: 0.3234 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2922 Z= 0.186 Angle : 0.622 9.427 3978 Z= 0.297 Chirality : 0.040 0.141 479 Planarity : 0.006 0.054 489 Dihedral : 5.199 52.863 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % 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: 2.13 (0.44), residues: 380 helix: 1.88 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.72 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.312 Fit side-chains REVERT: A 47 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6286 (t80) REVERT: A 230 MET cc_start: 0.7302 (ttt) cc_final: 0.7065 (ttm) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.1309 time to fit residues: 9.9779 Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126501 restraints weight = 3334.323| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.67 r_work: 0.3205 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2922 Z= 0.243 Angle : 0.650 9.591 3978 Z= 0.311 Chirality : 0.042 0.137 479 Planarity : 0.006 0.055 489 Dihedral : 5.196 51.610 407 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 21.67 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.44), residues: 380 helix: 1.82 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.54 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.277 Fit side-chains REVERT: A 47 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6254 (t80) REVERT: A 166 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 230 MET cc_start: 0.7310 (ttt) cc_final: 0.7080 (ttm) REVERT: A 433 TYR cc_start: 0.7716 (m-80) cc_final: 0.7417 (m-10) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.1172 time to fit residues: 8.9072 Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.149671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127326 restraints weight = 3395.895| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.76 r_work: 0.3185 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2922 Z= 0.258 Angle : 0.659 9.649 3978 Z= 0.316 Chirality : 0.042 0.133 479 Planarity : 0.006 0.055 489 Dihedral : 5.207 50.280 407 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 23.67 % Favored : 73.00 % 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: 2.03 (0.43), residues: 380 helix: 1.79 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.58 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.003 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.282 Fit side-chains REVERT: A 47 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6268 (t80) REVERT: A 166 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6934 (t80) REVERT: A 433 TYR cc_start: 0.7749 (m-80) cc_final: 0.7396 (m-10) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1209 time to fit residues: 8.2708 Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124443 restraints weight = 3437.268| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.71 r_work: 0.3189 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2922 Z= 0.252 Angle : 0.663 9.606 3978 Z= 0.317 Chirality : 0.042 0.131 479 Planarity : 0.006 0.054 489 Dihedral : 5.140 48.901 407 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 23.33 % Favored : 73.67 % 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: 1.91 (0.43), residues: 380 helix: 1.73 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -1.66 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.296 Fit side-chains REVERT: A 166 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6919 (t80) REVERT: A 230 MET cc_start: 0.7276 (ttt) cc_final: 0.7047 (ttm) REVERT: A 334 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: A 433 TYR cc_start: 0.7740 (m-80) cc_final: 0.7376 (m-10) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1233 time to fit residues: 8.4631 Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134423 restraints weight = 3367.163| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.59 r_work: 0.3206 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2922 Z= 0.243 Angle : 0.655 9.539 3978 Z= 0.313 Chirality : 0.041 0.133 479 Planarity : 0.006 0.057 489 Dihedral : 4.399 16.183 405 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.00 % Allowed : 22.33 % Favored : 73.67 % 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: 1.90 (0.44), residues: 380 helix: 1.73 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.71 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.292 Fit side-chains REVERT: A 166 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 230 MET cc_start: 0.7389 (ttt) cc_final: 0.6550 (tpt) REVERT: A 334 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: A 433 TYR cc_start: 0.7760 (m-80) cc_final: 0.7480 (m-10) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.1226 time to fit residues: 8.7337 Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135171 restraints weight = 3329.100| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.59 r_work: 0.3451 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2922 Z= 0.229 Angle : 0.647 9.467 3978 Z= 0.308 Chirality : 0.041 0.131 479 Planarity : 0.006 0.060 489 Dihedral : 4.361 16.354 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.33 % Allowed : 21.67 % Favored : 74.00 % 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: 1.97 (0.44), residues: 380 helix: 1.76 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.64 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.270 Fit side-chains REVERT: A 166 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 230 MET cc_start: 0.7715 (ttt) cc_final: 0.6962 (tpt) REVERT: A 334 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: A 433 TYR cc_start: 0.7922 (m-80) cc_final: 0.7682 (m-10) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.1319 time to fit residues: 9.3514 Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.0070 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137356 restraints weight = 3306.800| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.65 r_work: 0.3495 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2922 Z= 0.185 Angle : 0.623 9.133 3978 Z= 0.296 Chirality : 0.040 0.132 479 Planarity : 0.006 0.057 489 Dihedral : 4.211 15.210 405 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 23.00 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.44), residues: 380 helix: 1.92 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.60 (0.90), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.013 0.001 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.002 0.000 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.276 Fit side-chains REVERT: A 166 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 311 LEU cc_start: 0.8468 (tt) cc_final: 0.8073 (tt) REVERT: A 334 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6920 (m-80) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.1351 time to fit residues: 9.1720 Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133054 restraints weight = 3297.406| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.67 r_work: 0.3189 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2922 Z= 0.275 Angle : 0.667 9.634 3978 Z= 0.321 Chirality : 0.042 0.138 479 Planarity : 0.006 0.055 489 Dihedral : 4.477 16.128 405 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 23.33 % Favored : 73.33 % 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: 1.98 (0.44), residues: 380 helix: 1.74 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.49 (0.87), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.001 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.90 seconds wall clock time: 32 minutes 36.97 seconds (1956.97 seconds total)