Starting phenix.real_space_refine on Wed Mar 5 20:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.map" model { file = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2025/7lcj_23275.cif" } resolution = 2.82 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 571 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 3264 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 58 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 17} Link IDs: {None: 17} Time building chain proxies: 3.11, per 1000 atoms: 0.95 Number of scatterers: 3264 At special positions: 0 Unit cell: (60.079, 116.866, 69.955, 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 18 16.00 F 1 9.00 O 571 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 70.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.918A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.604A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 Processing helix chain 'R' and resid 202 through 207 removed outlier: 3.510A pdb=" N SER R 206 " --> pdb=" O LYS R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 3.944A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.705A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.800A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.848A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing helix chain 'R' and resid 377 through 392 Processing helix chain 'R' and resid 393 through 404 Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.547A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 597 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: 0.81 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 974 1.41 - 1.54: 1861 1.54 - 1.68: 6 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.44e-02 4.82e+03 1.17e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 4503 3.63 - 7.26: 63 7.26 - 10.88: 3 10.88 - 14.51: 1 14.51 - 18.14: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" C SER R 136 " pdb=" N PRO R 137 " pdb=" CA PRO R 137 " ideal model delta sigma weight residual 119.28 126.40 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta sigma weight residual 110.67 122.36 -11.69 1.92e+00 2.71e-01 3.71e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.12 18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C LEU R 89 " pdb=" N PRO R 90 " pdb=" CA PRO R 90 " ideal model delta sigma weight residual 119.28 125.52 -6.24 1.10e+00 8.26e-01 3.21e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.79 119.63 -8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1743 17.85 - 35.70: 157 35.70 - 53.55: 27 53.55 - 71.39: 3 71.39 - 89.24: 2 Dihedral angle restraints: 1932 sinusoidal: 776 harmonic: 1156 Sorted by residual: dihedral pdb=" C THR R 362 " pdb=" N THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta harmonic sigma weight residual -122.00 -143.04 21.04 0 2.50e+00 1.60e-01 7.08e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -142.72 56.72 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 466 0.145 - 0.290: 27 0.290 - 0.435: 2 0.435 - 0.580: 1 0.580 - 0.724: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR R 362 " pdb=" N THR R 362 " pdb=" C THR R 362 " pdb=" CB THR R 362 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA TRP R 243 " pdb=" N TRP R 243 " pdb=" C TRP R 243 " pdb=" CB TRP R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 355 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR R 355 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 355 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 356 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ILE R 146 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 277 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " 0.027 5.00e-02 4.00e+02 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 3196 3.29 - 3.83: 5221 3.83 - 4.36: 6319 4.36 - 4.90: 10614 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.216 3.120 nonbonded pdb=" O GLY R 98 " pdb=" ND1 HIS R 99 " model vdw 2.335 3.120 nonbonded pdb=" O GLU R 408 " pdb=" OE1 GLU R 412 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU R 76 " pdb=" OG SER R 79 " model vdw 2.342 3.040 nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.383 3.120 ... (remaining 25782 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=0.00 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.030 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.011 0.114 3351 Z= 0.669 Angle : 1.188 18.141 4571 Z= 0.785 Chirality : 0.083 0.724 497 Planarity : 0.006 0.049 557 Dihedral : 13.407 89.243 1172 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.67 % Cbeta Deviations : 0.80 % 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: 0.54 (0.41), residues: 386 helix: 1.08 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.006 0.002 HIS R 180 PHE 0.017 0.003 PHE R 280 TYR 0.023 0.003 TYR R 148 ARG 0.003 0.001 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.358 Fit side-chains REVERT: R 41 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6643 (mm-30) REVERT: R 416 SER cc_start: 0.6812 (t) cc_final: 0.6581 (m) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.9896 time to fit residues: 37.1424 Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.202849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132537 restraints weight = 3284.869| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.12 r_work: 0.3333 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.189 Angle : 0.589 7.195 4571 Z= 0.314 Chirality : 0.038 0.145 497 Planarity : 0.004 0.051 557 Dihedral : 5.304 30.069 458 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.45 % Allowed : 8.43 % Favored : 90.12 % 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: 1.55 (0.42), residues: 386 helix: 1.94 (0.32), residues: 255 sheet: None (None), residues: 0 loop : -0.82 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 PHE 0.014 0.002 PHE R 143 TYR 0.028 0.002 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.365 Fit side-chains REVERT: R 41 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6932 (mm-30) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.7993 time to fit residues: 27.9466 Evaluate side-chains 27 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.201997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131874 restraints weight = 3254.143| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.08 r_work: 0.3333 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3351 Z= 0.190 Angle : 0.549 10.065 4571 Z= 0.285 Chirality : 0.037 0.135 497 Planarity : 0.004 0.057 557 Dihedral : 4.859 30.723 456 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 11.05 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.43), residues: 386 helix: 2.22 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.67 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 243 HIS 0.006 0.001 HIS R 212 PHE 0.011 0.001 PHE R 280 TYR 0.027 0.002 TYR R 148 ARG 0.002 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.464 Fit side-chains REVERT: R 41 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6870 (mm-30) REVERT: R 201 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7289 (pt) REVERT: R 384 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7864 (mm) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.8675 time to fit residues: 24.7473 Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.202961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132731 restraints weight = 3293.528| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.10 r_work: 0.3333 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3351 Z= 0.167 Angle : 0.521 9.581 4571 Z= 0.271 Chirality : 0.037 0.128 497 Planarity : 0.004 0.059 557 Dihedral : 4.718 30.449 456 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.03 % Allowed : 13.08 % Favored : 84.88 % 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: 2.17 (0.43), residues: 386 helix: 2.43 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.64 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 243 HIS 0.002 0.001 HIS R 212 PHE 0.010 0.001 PHE R 280 TYR 0.026 0.001 TYR R 148 ARG 0.010 0.001 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.352 Fit side-chains REVERT: R 41 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6863 (mm-30) REVERT: R 201 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7191 (pt) REVERT: R 414 ARG cc_start: 0.6307 (mmt90) cc_final: 0.5266 (mmp-170) outliers start: 7 outliers final: 5 residues processed: 29 average time/residue: 0.8057 time to fit residues: 24.7622 Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.201845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131614 restraints weight = 3282.020| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.09 r_work: 0.3319 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3351 Z= 0.185 Angle : 0.528 9.719 4571 Z= 0.273 Chirality : 0.037 0.128 497 Planarity : 0.004 0.060 557 Dihedral : 4.699 31.221 456 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.20 % Allowed : 11.92 % Favored : 84.88 % 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: 2.15 (0.43), residues: 386 helix: 2.38 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 PHE 0.011 0.001 PHE R 280 TYR 0.026 0.002 TYR R 148 ARG 0.004 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.336 Fit side-chains REVERT: R 41 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6936 (mm-30) REVERT: R 201 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7232 (pt) REVERT: R 384 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (mm) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.6858 time to fit residues: 24.0718 Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.202676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132053 restraints weight = 3350.492| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.13 r_work: 0.3339 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3351 Z= 0.176 Angle : 0.515 9.595 4571 Z= 0.266 Chirality : 0.037 0.126 497 Planarity : 0.004 0.059 557 Dihedral : 4.638 30.782 456 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.20 % Allowed : 13.08 % Favored : 83.72 % 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 (0.43), residues: 386 helix: 2.48 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.65 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.003 0.001 HIS R 180 PHE 0.011 0.001 PHE R 280 TYR 0.025 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.369 Fit side-chains REVERT: R 41 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6921 (mm-30) REVERT: R 201 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7169 (pt) REVERT: R 384 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7890 (mm) outliers start: 11 outliers final: 6 residues processed: 33 average time/residue: 0.7136 time to fit residues: 25.0590 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.202444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132132 restraints weight = 3218.896| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.09 r_work: 0.3340 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3351 Z= 0.177 Angle : 0.513 9.611 4571 Z= 0.265 Chirality : 0.036 0.127 497 Planarity : 0.004 0.059 557 Dihedral : 4.622 31.110 456 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.91 % Allowed : 13.95 % Favored : 83.14 % 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: 2.33 (0.43), residues: 386 helix: 2.50 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.54 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 PHE 0.010 0.001 PHE R 280 TYR 0.025 0.001 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.364 Fit side-chains REVERT: R 41 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6953 (mm-30) REVERT: R 201 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7202 (pt) REVERT: R 384 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7915 (mm) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.6572 time to fit residues: 23.1661 Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.0030 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.205346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132845 restraints weight = 3288.867| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3349 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.153 Angle : 0.494 9.267 4571 Z= 0.255 Chirality : 0.036 0.123 497 Planarity : 0.004 0.058 557 Dihedral : 4.531 30.400 456 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.03 % Allowed : 15.12 % Favored : 82.85 % 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: 2.49 (0.43), residues: 386 helix: 2.63 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.50 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.002 0.000 HIS R 180 PHE 0.009 0.001 PHE R 280 TYR 0.024 0.001 TYR R 148 ARG 0.006 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.360 Fit side-chains REVERT: R 41 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6903 (mm-30) REVERT: R 384 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7837 (mm) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.7760 time to fit residues: 24.9347 Evaluate side-chains 32 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.0000 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.205797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136279 restraints weight = 3284.976| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.09 r_work: 0.3393 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.132 Angle : 0.464 7.096 4571 Z= 0.242 Chirality : 0.035 0.118 497 Planarity : 0.004 0.058 557 Dihedral : 4.415 29.855 456 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.74 % Allowed : 15.41 % Favored : 82.85 % 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: 2.70 (0.43), residues: 386 helix: 2.82 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.49 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.001 0.000 HIS R 212 PHE 0.008 0.001 PHE R 324 TYR 0.024 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.355 Fit side-chains REVERT: R 41 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6940 (mm-30) REVERT: R 384 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7813 (mm) REVERT: R 397 MET cc_start: 0.8198 (mtt) cc_final: 0.7402 (mmp) REVERT: R 414 ARG cc_start: 0.6313 (mmt90) cc_final: 0.6038 (mtt90) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.6944 time to fit residues: 22.1583 Evaluate side-chains 31 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.206507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137359 restraints weight = 3217.777| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.08 r_work: 0.3406 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3351 Z= 0.131 Angle : 0.480 9.159 4571 Z= 0.247 Chirality : 0.035 0.133 497 Planarity : 0.004 0.059 557 Dihedral : 4.330 29.573 456 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 15.70 % Favored : 82.56 % 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: 2.77 (0.43), residues: 386 helix: 2.89 (0.32), residues: 260 sheet: None (None), residues: 0 loop : -0.51 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.001 0.000 HIS R 212 PHE 0.008 0.001 PHE R 324 TYR 0.023 0.001 TYR R 148 ARG 0.006 0.000 ARG R 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.338 Fit side-chains REVERT: R 41 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6869 (mm-30) REVERT: R 201 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7078 (pp) REVERT: R 384 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7790 (mm) REVERT: R 397 MET cc_start: 0.8109 (mtt) cc_final: 0.7308 (mmp) REVERT: R 414 ARG cc_start: 0.6218 (mmt90) cc_final: 0.5951 (mtt90) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.7432 time to fit residues: 24.4154 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.203553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133591 restraints weight = 3256.367| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.10 r_work: 0.3354 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3351 Z= 0.171 Angle : 0.502 9.205 4571 Z= 0.259 Chirality : 0.036 0.131 497 Planarity : 0.004 0.058 557 Dihedral : 4.482 30.990 456 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 16.57 % Favored : 81.69 % 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: 2.63 (0.43), residues: 386 helix: 2.76 (0.31), residues: 260 sheet: None (None), residues: 0 loop : -0.49 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.010 0.001 PHE R 280 TYR 0.025 0.001 TYR R 148 ARG 0.007 0.000 ARG R 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.75 seconds wall clock time: 51 minutes 46.63 seconds (3106.63 seconds total)