Starting phenix.real_space_refine on Wed Mar 5 18:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zne_60269/03_2025/8zne_60269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zne_60269/03_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_60269/03_2025/8zne_60269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zne_60269/03_2025/8zne_60269.map" model { file = "/net/cci-nas-00/data/ceres_data/8zne_60269/03_2025/8zne_60269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zne_60269/03_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-5624/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: 2.61, per 1000 atoms: 0.79 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: 0.72 Conformation dependent library (CDL) restraints added in 352.0 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: 0.33 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: 0.88 Time building geometry restraints manager: 0.89 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- 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 : 0.337 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: 1.3698 time to fit residues: 129.1178 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 : 0.347 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105765 restraints weight = 4107.932| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.60 r_work: 0.2962 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3376 Z= 0.202 Angle : 0.522 6.396 4581 Z= 0.279 Chirality : 0.044 0.132 498 Planarity : 0.005 0.048 584 Dihedral : 10.469 62.801 496 Min Nonbonded Distance : 2.493 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: 1.97 (0.36), residues: 209 sheet: -0.18 (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 30 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 0.002 0.000 ARG A 265 *********************** 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 : 0.372 Fit side-chains REVERT: A 9 MET cc_start: 0.7880 (mtp) cc_final: 0.7329 (mtm) REVERT: A 327 ASP cc_start: 0.8198 (m-30) cc_final: 0.7994 (m-30) outliers start: 10 outliers final: 1 residues processed: 70 average time/residue: 1.3509 time to fit residues: 97.0887 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 : 0.373 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096905 restraints weight = 4152.725| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.59 r_work: 0.2842 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3376 Z= 0.357 Angle : 0.578 5.544 4581 Z= 0.313 Chirality : 0.047 0.133 498 Planarity : 0.005 0.049 584 Dihedral : 9.437 57.606 490 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 16.76 % Favored : 80.59 % 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: 0.65 (0.42), residues: 414 helix: 1.73 (0.36), residues: 211 sheet: -0.22 (0.80), residues: 52 loop : -1.21 (0.48), 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 0.018 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 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.405 Fit side-chains REVERT: A 9 MET cc_start: 0.7999 (mtp) cc_final: 0.7474 (mtm) REVERT: A 12 LYS cc_start: 0.8324 (tttp) cc_final: 0.7843 (ttpp) REVERT: A 244 ASP cc_start: 0.7473 (t0) cc_final: 0.7143 (t0) REVERT: A 287 LEU cc_start: 0.8101 (tt) cc_final: 0.7865 (tt) REVERT: A 370 ARG cc_start: 0.7159 (ttt-90) cc_final: 0.6225 (ttm170) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 1.4330 time to fit residues: 95.5790 Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.133913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102879 restraints weight = 4233.656| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.61 r_work: 0.2942 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3376 Z= 0.144 Angle : 0.466 4.574 4581 Z= 0.248 Chirality : 0.042 0.123 498 Planarity : 0.005 0.049 584 Dihedral : 8.632 57.989 490 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.06 % Allowed : 19.71 % 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: 0.89 (0.42), residues: 414 helix: 1.93 (0.35), residues: 213 sheet: 0.13 (0.86), residues: 47 loop : -1.23 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 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 69 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.346 Fit side-chains REVERT: A 9 MET cc_start: 0.7961 (mtp) cc_final: 0.7442 (mtm) REVERT: A 244 ASP cc_start: 0.7633 (t0) cc_final: 0.7215 (t0) REVERT: A 370 ARG cc_start: 0.7102 (ttt-90) cc_final: 0.6189 (ttm170) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 1.5122 time to fit residues: 105.3278 Evaluate side-chains 61 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 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: 1.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101035 restraints weight = 4187.680| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.61 r_work: 0.2902 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3499 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= 0.181 Angle : 0.493 5.173 4581 Z= 0.261 Chirality : 0.043 0.127 498 Planarity : 0.004 0.047 584 Dihedral : 8.373 59.917 490 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.24 % Allowed : 20.00 % Favored : 76.76 % 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: 1.10 (0.42), residues: 414 helix: 2.09 (0.35), residues: 212 sheet: 0.50 (0.77), residues: 57 loop : -1.30 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 HIS 0.004 0.001 HIS A 394 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 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 69 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8008 (mtp) cc_final: 0.7502 (mtm) REVERT: A 12 LYS cc_start: 0.8355 (tttp) cc_final: 0.7837 (ttpp) REVERT: A 244 ASP cc_start: 0.7675 (t0) cc_final: 0.7162 (t0) REVERT: A 370 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6253 (ttm170) REVERT: A 388 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8539 (t70) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 1.3912 time to fit residues: 92.7390 Evaluate side-chains 63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 4 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104891 restraints weight = 4269.597| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.63 r_work: 0.2964 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3376 Z= 0.126 Angle : 0.451 4.991 4581 Z= 0.234 Chirality : 0.042 0.125 498 Planarity : 0.004 0.047 584 Dihedral : 7.873 59.701 490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.24 % Allowed : 20.29 % Favored : 76.47 % 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: 2.19 (0.35), residues: 213 sheet: 0.44 (0.76), residues: 57 loop : -1.32 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS A 394 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 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 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7970 (mtp) cc_final: 0.7479 (mtm) REVERT: A 167 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8852 (mmpt) REVERT: A 244 ASP cc_start: 0.7747 (t0) cc_final: 0.7173 (t0) REVERT: A 272 ASP cc_start: 0.7360 (m-30) cc_final: 0.6845 (m-30) REVERT: A 370 ARG cc_start: 0.7134 (ttt-90) cc_final: 0.6230 (ttm170) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 1.4285 time to fit residues: 95.0992 Evaluate side-chains 60 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 332 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: 0.8980 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.133242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102251 restraints weight = 4199.605| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.61 r_work: 0.2938 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3376 Z= 0.171 Angle : 0.497 5.032 4581 Z= 0.259 Chirality : 0.043 0.127 498 Planarity : 0.004 0.046 584 Dihedral : 7.773 59.893 490 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 2.21 (0.35), residues: 212 sheet: 0.45 (0.76), residues: 57 loop : -1.30 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 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 0.001 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 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7989 (mtp) cc_final: 0.7503 (mtm) REVERT: A 167 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8894 (mmpt) REVERT: A 244 ASP cc_start: 0.7757 (t0) cc_final: 0.7535 (t0) REVERT: A 370 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6220 (ttm170) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 1.4112 time to fit residues: 92.6616 Evaluate side-chains 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 149 ASN 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 303 GLU Chi-restraints excluded: chain A residue 332 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: 0.4980 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.135926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104963 restraints weight = 4171.727| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.61 r_work: 0.2970 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3376 Z= 0.130 Angle : 0.460 6.164 4581 Z= 0.240 Chirality : 0.042 0.126 498 Planarity : 0.004 0.047 584 Dihedral : 7.470 57.944 490 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.35 % Allowed : 21.76 % 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: 1.20 (0.42), residues: 414 helix: 2.25 (0.35), residues: 213 sheet: 0.44 (0.76), residues: 57 loop : -1.36 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** 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 69 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.375 Fit side-chains REVERT: A 9 MET cc_start: 0.7922 (mtp) cc_final: 0.7443 (mtm) REVERT: A 208 ILE cc_start: 0.6202 (pt) cc_final: 0.6000 (pp) REVERT: A 244 ASP cc_start: 0.7769 (t0) cc_final: 0.7506 (t0) REVERT: A 272 ASP cc_start: 0.7368 (m-30) cc_final: 0.6861 (m-30) REVERT: A 370 ARG cc_start: 0.7132 (ttt-90) cc_final: 0.6238 (ttm170) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 1.4795 time to fit residues: 100.1089 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 : 0.361 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.132537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101225 restraints weight = 4222.448| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.63 r_work: 0.2908 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3376 Z= 0.180 Angle : 0.492 6.190 4581 Z= 0.259 Chirality : 0.043 0.126 498 Planarity : 0.004 0.045 584 Dihedral : 7.571 58.909 490 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.35 % Allowed : 21.18 % Favored : 76.47 % 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: 1.15 (0.42), residues: 414 helix: 2.23 (0.35), residues: 212 sheet: 0.45 (0.76), residues: 57 loop : -1.42 (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 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** 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: 8 poor density : 60 time to evaluate : 0.394 Fit side-chains REVERT: A 9 MET cc_start: 0.8012 (mtp) cc_final: 0.7534 (mtm) REVERT: A 208 ILE cc_start: 0.6267 (pt) cc_final: 0.6022 (pp) REVERT: A 244 ASP cc_start: 0.7783 (t0) cc_final: 0.7464 (t0) REVERT: A 370 ARG cc_start: 0.7164 (ttt-90) cc_final: 0.6244 (ttm170) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 1.3788 time to fit residues: 91.9552 Evaluate side-chains 65 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.0040 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 = 0.135912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.105248 restraints weight = 4201.851| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.58 r_work: 0.2957 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3376 Z= 0.136 Angle : 0.469 5.556 4581 Z= 0.244 Chirality : 0.042 0.125 498 Planarity : 0.004 0.047 584 Dihedral : 7.382 57.489 490 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.76 % Allowed : 21.76 % Favored : 76.47 % 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: 2.26 (0.35), residues: 213 sheet: 0.49 (0.75), residues: 57 loop : -1.45 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.000 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 ********************** 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 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.324 Fit side-chains REVERT: A 9 MET cc_start: 0.7858 (mtp) cc_final: 0.7355 (mtm) REVERT: A 208 ILE cc_start: 0.6191 (pt) cc_final: 0.5936 (pp) REVERT: A 244 ASP cc_start: 0.7757 (t0) cc_final: 0.7415 (t0) REVERT: A 272 ASP cc_start: 0.7410 (m-30) cc_final: 0.6881 (m-30) REVERT: A 370 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6140 (ttm170) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 1.4445 time to fit residues: 91.7756 Evaluate side-chains 62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.134207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.103258 restraints weight = 4224.494| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.62 r_work: 0.2936 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3376 Z= 0.151 Angle : 0.484 6.720 4581 Z= 0.252 Chirality : 0.042 0.127 498 Planarity : 0.004 0.046 584 Dihedral : 7.323 57.355 490 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.18 % Allowed : 22.65 % 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: 1.19 (0.42), residues: 414 helix: 2.28 (0.35), residues: 212 sheet: 0.50 (0.75), residues: 57 loop : -1.45 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 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: 3107.67 seconds wall clock time: 53 minutes 54.86 seconds (3234.86 seconds total)