Starting phenix.real_space_refine on Mon Jan 13 16:52:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.map" model { file = "/net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zne_60269/01_2025/8zne_60269.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2098 2.51 5 N 562 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 50 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 501 "'] Classifications: {'peptide': 1, 'undetermined': 1, 'water': 9} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.17, per 1000 atoms: 0.96 Number of scatterers: 3312 At special positions: 0 Unit cell: (66.176, 66.176, 71.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 635 8.00 N 562 7.00 C 2098 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: 0.81 Conformation dependent library (CDL) restraints added in 385.4 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 54.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.749A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.800A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.512A pdb=" N ARG A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.569A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.666A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.902A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 519 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: 0.97 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 589 1.32 - 1.44: 837 1.44 - 1.57: 1918 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3376 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.610 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C THR A 280 " pdb=" N ASN A 281 " ideal model delta sigma weight residual 1.334 1.420 -0.086 1.43e-02 4.89e+03 3.58e+01 bond pdb=" N GLY A 254 " pdb=" CA GLY A 254 " ideal model delta sigma weight residual 1.448 1.476 -0.028 8.80e-03 1.29e+04 1.01e+01 bond pdb=" C PRO A 321 " pdb=" O PRO A 321 " ideal model delta sigma weight residual 1.239 1.200 0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" C ASP A 327 " pdb=" N ASP A 328 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.36e-02 5.41e+03 8.11e+00 ... (remaining 3371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4346 1.61 - 3.23: 194 3.23 - 4.84: 34 4.84 - 6.46: 5 6.46 - 8.07: 2 Bond angle restraints: 4581 Sorted by residual: angle pdb=" CA GLY A 254 " pdb=" C GLY A 254 " pdb=" O GLY A 254 " ideal model delta sigma weight residual 122.37 118.22 4.15 7.30e-01 1.88e+00 3.24e+01 angle pdb=" CA LYS A 376 " pdb=" C LYS A 376 " pdb=" O LYS A 376 " ideal model delta sigma weight residual 120.42 115.73 4.69 1.06e+00 8.90e-01 1.95e+01 angle pdb=" C SER A 269 " pdb=" CA SER A 269 " pdb=" CB SER A 269 " ideal model delta sigma weight residual 115.89 110.23 5.66 1.32e+00 5.74e-01 1.84e+01 angle pdb=" C PHE A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta sigma weight residual 119.24 123.04 -3.80 1.04e+00 9.25e-01 1.33e+01 angle pdb=" CA LYS A 376 " pdb=" C LYS A 376 " pdb=" N MET A 377 " ideal model delta sigma weight residual 117.39 121.57 -4.18 1.24e+00 6.50e-01 1.14e+01 ... (remaining 4576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 1827 16.79 - 33.59: 129 33.59 - 50.38: 51 50.38 - 67.18: 21 67.18 - 83.97: 14 Dihedral angle restraints: 2042 sinusoidal: 851 harmonic: 1191 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PHE A 341 " pdb=" C PHE A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta harmonic sigma weight residual 180.00 164.49 15.51 0 5.00e+00 4.00e-02 9.62e+00 dihedral pdb=" CA ASP A 390 " pdb=" CB ASP A 390 " pdb=" CG ASP A 390 " pdb=" OD1 ASP A 390 " ideal model delta sinusoidal sigma weight residual -30.00 -83.03 53.03 1 2.00e+01 2.50e-03 9.57e+00 ... (remaining 2039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 317 0.034 - 0.068: 117 0.068 - 0.102: 36 0.102 - 0.136: 22 0.136 - 0.170: 6 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB ARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA LEU A 255 " pdb=" N LEU A 255 " pdb=" C LEU A 255 " pdb=" CB LEU A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL A 239 " pdb=" N VAL A 239 " pdb=" C VAL A 239 " pdb=" CB VAL A 239 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 495 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 150 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 318 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ALA A 318 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 318 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 319 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 142 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1466 2.96 - 3.44: 3466 3.44 - 3.93: 5883 3.93 - 4.41: 6798 4.41 - 4.90: 10699 Nonbonded interactions: 28312 Sorted by model distance: nonbonded pdb=" OG SER A 351 " pdb=" OE1 GLU A 501 " model vdw 2.472 3.040 nonbonded pdb=" NH2 ARG A 200 " pdb=" OD1 ASP A 374 " model vdw 2.477 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.481 3.120 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.496 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OE1 GLU A 266 " model vdw 2.531 3.040 ... (remaining 28307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.040 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.126 3376 Z= 0.317 Angle : 0.778 8.071 4581 Z= 0.498 Chirality : 0.047 0.170 498 Planarity : 0.005 0.048 584 Dihedral : 16.818 83.970 1282 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 2.35 % Favored : 95.00 % 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: 0.47 (0.41), residues: 414 helix: 1.63 (0.35), residues: 208 sheet: 0.04 (0.68), residues: 65 loop : -1.59 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.003 0.001 HIS A 388 PHE 0.015 0.002 PHE A 273 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.370 Fit side-chains REVERT: A 9 MET cc_start: 0.7369 (mtp) cc_final: 0.7091 (mtm) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 1.4890 time to fit residues: 140.2579 Evaluate side-chains 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.137962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106369 restraints weight = 4103.499| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.58 r_work: 0.2955 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3376 Z= 0.207 Angle : 0.523 6.507 4581 Z= 0.280 Chirality : 0.044 0.146 498 Planarity : 0.005 0.047 584 Dihedral : 10.567 63.424 496 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.94 % Allowed : 13.82 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.43), residues: 414 helix: 1.98 (0.36), residues: 209 sheet: -0.19 (0.75), residues: 57 loop : -1.34 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.471 Fit side-chains REVERT: A 9 MET cc_start: 0.7811 (mtp) cc_final: 0.7250 (mtm) REVERT: A 327 ASP cc_start: 0.8175 (m-30) cc_final: 0.7965 (m-30) outliers start: 10 outliers final: 1 residues processed: 70 average time/residue: 1.3881 time to fit residues: 99.8257 Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.096342 restraints weight = 4110.383| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.59 r_work: 0.2854 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3376 Z= 0.351 Angle : 0.571 5.341 4581 Z= 0.309 Chirality : 0.047 0.131 498 Planarity : 0.005 0.048 584 Dihedral : 9.441 57.373 490 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.42), residues: 414 helix: 1.73 (0.35), residues: 211 sheet: -0.24 (0.79), residues: 52 loop : -1.21 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 355 HIS 0.007 0.001 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.016 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.398 Fit side-chains REVERT: A 9 MET cc_start: 0.8008 (mtp) cc_final: 0.7482 (mtm) REVERT: A 12 LYS cc_start: 0.8335 (tttp) cc_final: 0.7859 (ttpp) REVERT: A 244 ASP cc_start: 0.7479 (t0) cc_final: 0.7126 (t0) REVERT: A 287 LEU cc_start: 0.8073 (tt) cc_final: 0.7866 (tt) REVERT: A 327 ASP cc_start: 0.8354 (m-30) cc_final: 0.8151 (m-30) REVERT: A 370 ARG cc_start: 0.7163 (ttt-90) cc_final: 0.6203 (ttm170) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 1.4566 time to fit residues: 97.1714 Evaluate side-chains 59 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.1980 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104598 restraints weight = 4212.337| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.58 r_work: 0.2958 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3376 Z= 0.139 Angle : 0.466 4.034 4581 Z= 0.248 Chirality : 0.042 0.135 498 Planarity : 0.004 0.049 584 Dihedral : 8.635 58.035 490 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 19.12 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.42), residues: 414 helix: 1.96 (0.35), residues: 213 sheet: 0.08 (0.85), residues: 47 loop : -1.29 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.353 Fit side-chains REVERT: A 9 MET cc_start: 0.7976 (mtp) cc_final: 0.7458 (mtm) REVERT: A 244 ASP cc_start: 0.7627 (t0) cc_final: 0.7169 (t0) REVERT: A 287 LEU cc_start: 0.7891 (tt) cc_final: 0.7672 (tt) REVERT: A 304 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8119 (tppp) REVERT: A 327 ASP cc_start: 0.8186 (m-30) cc_final: 0.7981 (m-30) REVERT: A 370 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.6168 (ttm170) outliers start: 9 outliers final: 3 residues processed: 70 average time/residue: 1.6199 time to fit residues: 116.0197 Evaluate side-chains 59 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.130799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100843 restraints weight = 4210.903| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.54 r_work: 0.2867 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3376 Z= 0.341 Angle : 0.560 5.589 4581 Z= 0.302 Chirality : 0.047 0.129 498 Planarity : 0.005 0.048 584 Dihedral : 8.964 56.405 490 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 19.41 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.41), residues: 414 helix: 1.92 (0.35), residues: 211 sheet: -0.24 (0.80), residues: 52 loop : -1.33 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.007 0.002 HIS A 394 PHE 0.016 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.422 Fit side-chains REVERT: A 9 MET cc_start: 0.8056 (mtp) cc_final: 0.7571 (mtm) REVERT: A 12 LYS cc_start: 0.8448 (tttp) cc_final: 0.7968 (ttpp) REVERT: A 304 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8180 (tppp) REVERT: A 370 ARG cc_start: 0.7183 (ttt-90) cc_final: 0.6277 (ttm170) REVERT: A 388 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8490 (t70) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 1.4952 time to fit residues: 104.1205 Evaluate side-chains 65 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.134708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104106 restraints weight = 4294.754| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.61 r_work: 0.2944 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3376 Z= 0.120 Angle : 0.445 5.398 4581 Z= 0.235 Chirality : 0.042 0.126 498 Planarity : 0.004 0.049 584 Dihedral : 8.231 59.198 490 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.94 % Allowed : 20.88 % Favored : 76.18 % 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: 1.06 (0.42), residues: 414 helix: 2.12 (0.35), residues: 213 sheet: 0.43 (0.77), residues: 57 loop : -1.41 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 394 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 408 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.338 Fit side-chains REVERT: A 9 MET cc_start: 0.7978 (mtp) cc_final: 0.7469 (mtm) REVERT: A 167 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8854 (mmpt) REVERT: A 208 ILE cc_start: 0.6294 (pt) cc_final: 0.6093 (pp) REVERT: A 244 ASP cc_start: 0.7662 (t0) cc_final: 0.7192 (t0) REVERT: A 272 ASP cc_start: 0.7564 (t0) cc_final: 0.6860 (m-30) REVERT: A 370 ARG cc_start: 0.7130 (ttt-90) cc_final: 0.6229 (ttm170) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 1.4898 time to fit residues: 97.6401 Evaluate side-chains 61 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.0030 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106737 restraints weight = 4177.686| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.58 r_work: 0.2976 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3376 Z= 0.130 Angle : 0.465 5.542 4581 Z= 0.242 Chirality : 0.042 0.126 498 Planarity : 0.004 0.047 584 Dihedral : 7.755 59.455 490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.94 % Allowed : 21.18 % Favored : 75.88 % 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: 1.18 (0.42), residues: 414 helix: 2.24 (0.35), residues: 213 sheet: 0.49 (0.76), residues: 57 loop : -1.40 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 408 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.574 Fit side-chains REVERT: A 9 MET cc_start: 0.7920 (mtp) cc_final: 0.7424 (mtm) REVERT: A 208 ILE cc_start: 0.6284 (pt) cc_final: 0.6082 (pp) REVERT: A 244 ASP cc_start: 0.7769 (t0) cc_final: 0.7239 (t0) REVERT: A 272 ASP cc_start: 0.7545 (t0) cc_final: 0.6823 (m-30) REVERT: A 370 ARG cc_start: 0.7114 (ttt-90) cc_final: 0.6214 (ttm170) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 1.4564 time to fit residues: 100.1099 Evaluate side-chains 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 1.9722 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.132058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101075 restraints weight = 4192.001| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.58 r_work: 0.2895 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3376 Z= 0.213 Angle : 0.503 5.579 4581 Z= 0.265 Chirality : 0.044 0.125 498 Planarity : 0.004 0.046 584 Dihedral : 7.913 59.365 490 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.06 % Allowed : 22.35 % Favored : 75.59 % 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: 1.11 (0.42), residues: 414 helix: 2.21 (0.35), residues: 212 sheet: 0.47 (0.76), residues: 57 loop : -1.47 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.391 Fit side-chains REVERT: A 9 MET cc_start: 0.8046 (mtp) cc_final: 0.7555 (mtm) REVERT: A 208 ILE cc_start: 0.6355 (pt) cc_final: 0.6126 (pp) REVERT: A 244 ASP cc_start: 0.7749 (t0) cc_final: 0.7481 (t0) REVERT: A 370 ARG cc_start: 0.7173 (ttt-90) cc_final: 0.6279 (ttm170) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 1.5564 time to fit residues: 100.4260 Evaluate side-chains 63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104999 restraints weight = 4223.233| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.59 r_work: 0.2962 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3376 Z= 0.144 Angle : 0.482 6.635 4581 Z= 0.251 Chirality : 0.042 0.127 498 Planarity : 0.004 0.047 584 Dihedral : 7.607 58.426 490 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.06 % Allowed : 22.06 % Favored : 75.88 % 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: 1.17 (0.42), residues: 414 helix: 2.24 (0.35), residues: 213 sheet: 0.52 (0.76), residues: 57 loop : -1.47 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.001 0.000 HIS A 394 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.365 Fit side-chains REVERT: A 9 MET cc_start: 0.7931 (mtp) cc_final: 0.7439 (mtm) REVERT: A 208 ILE cc_start: 0.6297 (pt) cc_final: 0.6062 (pp) REVERT: A 244 ASP cc_start: 0.7776 (t0) cc_final: 0.7488 (t0) REVERT: A 370 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6162 (ttm170) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.5720 time to fit residues: 103.0862 Evaluate side-chains 62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.135994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105091 restraints weight = 4195.854| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.60 r_work: 0.2957 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3376 Z= 0.138 Angle : 0.481 7.212 4581 Z= 0.249 Chirality : 0.042 0.128 498 Planarity : 0.004 0.047 584 Dihedral : 7.268 56.863 490 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.47 % Allowed : 23.24 % Favored : 75.29 % 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: 1.22 (0.42), residues: 414 helix: 2.32 (0.35), residues: 212 sheet: 0.55 (0.76), residues: 57 loop : -1.48 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.378 Fit side-chains REVERT: A 9 MET cc_start: 0.7904 (mtp) cc_final: 0.7417 (mtm) REVERT: A 208 ILE cc_start: 0.6244 (pt) cc_final: 0.5993 (pp) REVERT: A 244 ASP cc_start: 0.7801 (t0) cc_final: 0.7427 (t0) REVERT: A 304 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8064 (tppp) REVERT: A 370 ARG cc_start: 0.7122 (ttt-90) cc_final: 0.6225 (ttm170) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 1.6629 time to fit residues: 107.2623 Evaluate side-chains 63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.135915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105020 restraints weight = 4221.566| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3376 Z= 0.144 Angle : 0.490 7.047 4581 Z= 0.253 Chirality : 0.042 0.126 498 Planarity : 0.004 0.047 584 Dihedral : 7.182 56.379 490 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.76 % Allowed : 23.24 % 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: 1.20 (0.42), residues: 414 helix: 2.33 (0.35), residues: 212 sheet: 0.55 (0.76), residues: 57 loop : -1.52 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.72 seconds wall clock time: 57 minutes 28.22 seconds (3448.22 seconds total)