Starting phenix.real_space_refine on Wed Mar 5 19:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.map" model { file = "/net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znd_60268/03_2025/8znd_60268.cif" } resolution = 2.53 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 2104 2.51 5 N 563 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 3334 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 72 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} Time building chain proxies: 2.75, per 1000 atoms: 0.82 Number of scatterers: 3334 At special positions: 0 Unit cell: (66.176, 63.92, 70.688, 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 650 8.00 N 563 7.00 C 2104 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: 0.83 Conformation dependent library (CDL) restraints added in 398.4 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: 758 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 56.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 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: 3.681A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 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: 3.551A 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 removed outlier: 3.728A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.556A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 removed outlier: 4.023A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (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: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.558A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 555 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: 0.94 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1069 1.34 - 1.46: 465 1.46 - 1.57: 1820 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3386 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.607 0.226 3.80e-02 6.93e+02 3.53e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.596 0.161 3.50e-02 8.16e+02 2.13e+01 bond pdb=" N TYR A 250 " pdb=" CA TYR A 250 " ideal model delta sigma weight residual 1.455 1.413 0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.90e-02 1.19e+03 9.52e+00 bond pdb=" CA TYR A 250 " pdb=" C TYR A 250 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.22e-02 6.72e+03 7.60e+00 ... (remaining 3381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 4575 4.44 - 8.88: 19 8.88 - 13.31: 1 13.31 - 17.75: 2 17.75 - 22.19: 1 Bond angle restraints: 4598 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 129.93 -22.19 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.43 -15.59 1.91e+00 2.73e-01 6.63e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 118.60 -13.67 2.66e+00 1.41e-01 2.64e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.34 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.28 5.18 1.17e+00 7.36e-01 1.97e+01 ... (remaining 4593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 1872 23.43 - 46.87: 110 46.87 - 70.30: 17 70.30 - 93.73: 9 93.73 - 117.16: 1 Dihedral angle restraints: 2009 sinusoidal: 820 harmonic: 1189 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 57.88 117.16 1 3.00e+01 1.11e-03 1.55e+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 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -89.63 89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 381 0.047 - 0.093: 79 0.093 - 0.140: 36 0.140 - 0.186: 2 0.186 - 0.233: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR A 250 " pdb=" N TYR A 250 " pdb=" C TYR A 250 " pdb=" CB TYR A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 498 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " 0.018 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C5N NDP A 500 " -0.039 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " 0.040 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.031 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" C3N NDP A 500 " 0.004 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.005 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.016 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 142 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1217 2.89 - 3.39: 3334 3.39 - 3.90: 6075 3.90 - 4.40: 6964 4.40 - 4.90: 11339 Nonbonded interactions: 28929 Sorted by model distance: nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.392 3.120 nonbonded pdb=" O VAL A 401 " pdb=" OG SER A 405 " model vdw 2.402 3.040 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.440 3.040 nonbonded pdb=" N ASP A 145 " pdb=" OG1 THR A 148 " model vdw 2.495 3.120 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.504 3.120 ... (remaining 28924 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: 0.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:21.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 : 0.007 0.226 3386 Z= 0.501 Angle : 0.927 22.188 4598 Z= 0.525 Chirality : 0.048 0.233 501 Planarity : 0.005 0.047 586 Dihedral : 15.596 117.160 1251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 0.59 % Favored : 98.53 % 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: 0.95 (0.42), residues: 414 helix: 2.03 (0.35), residues: 202 sheet: -0.23 (0.63), residues: 72 loop : -0.97 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 61 PHE 0.015 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.004 0.000 ARG A 58 *********************** 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 86 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.457 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 1.5264 time to fit residues: 131.2342 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 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 = 0.3271 r_free = 0.3271 target = 0.115085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090272 restraints weight = 4082.138| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.53 r_work: 0.2757 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3386 Z= 0.159 Angle : 0.469 4.404 4598 Z= 0.250 Chirality : 0.042 0.129 501 Planarity : 0.005 0.044 586 Dihedral : 6.552 99.326 462 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.47 % Allowed : 11.21 % Favored : 87.32 % 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: 2.04 (0.35), residues: 208 sheet: -0.00 (0.65), residues: 73 loop : -0.95 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.014 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.006 0.001 ARG A 370 *********************** 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 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.345 Fit side-chains REVERT: A 271 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8933 (ttmt) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 1.4641 time to fit residues: 106.6251 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.109886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.084919 restraints weight = 4061.793| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.52 r_work: 0.2653 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3386 Z= 0.270 Angle : 0.511 4.566 4598 Z= 0.273 Chirality : 0.044 0.132 501 Planarity : 0.005 0.048 586 Dihedral : 6.512 90.264 462 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 14.45 % Favored : 84.66 % 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: 1.04 (0.42), residues: 414 helix: 1.95 (0.35), residues: 209 sheet: 0.00 (0.64), residues: 72 loop : -0.93 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.016 0.002 TYR A 363 ARG 0.007 0.001 ARG A 265 *********************** 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 60 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.380 Fit side-chains REVERT: A 21 MET cc_start: 0.8906 (ptm) cc_final: 0.8647 (ptt) REVERT: A 246 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8001 (mpt180) outliers start: 3 outliers final: 0 residues processed: 59 average time/residue: 1.6514 time to fit residues: 99.6432 Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.109049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.083999 restraints weight = 4098.376| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.54 r_work: 0.2639 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3386 Z= 0.298 Angle : 0.520 4.633 4598 Z= 0.277 Chirality : 0.045 0.130 501 Planarity : 0.006 0.057 586 Dihedral : 6.433 86.197 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.36 % Allowed : 12.98 % Favored : 84.66 % 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: 0.95 (0.42), residues: 414 helix: 1.90 (0.35), residues: 208 sheet: -0.02 (0.64), residues: 72 loop : -1.00 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.016 0.002 TYR A 363 ARG 0.007 0.001 ARG A 265 *********************** 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 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.342 Fit side-chains REVERT: A 21 MET cc_start: 0.8969 (ptm) cc_final: 0.8595 (ptt) REVERT: A 78 GLU cc_start: 0.8916 (tp30) cc_final: 0.8668 (tp30) REVERT: A 246 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8202 (mpt180) REVERT: A 332 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8325 (tm-30) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 1.5258 time to fit residues: 89.0703 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.085662 restraints weight = 4155.553| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.54 r_work: 0.2684 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3386 Z= 0.203 Angle : 0.467 4.514 4598 Z= 0.249 Chirality : 0.043 0.131 501 Planarity : 0.005 0.048 586 Dihedral : 6.196 82.941 462 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.36 % Allowed : 13.86 % Favored : 83.78 % 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: 1.03 (0.42), residues: 414 helix: 2.02 (0.35), residues: 208 sheet: -0.10 (0.65), residues: 73 loop : -1.00 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.005 0.000 ARG A 370 *********************** 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 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.384 Fit side-chains REVERT: A 21 MET cc_start: 0.8978 (ptm) cc_final: 0.8669 (ptt) REVERT: A 78 GLU cc_start: 0.8902 (tp30) cc_final: 0.8681 (tp30) REVERT: A 246 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8374 (mpt180) REVERT: A 332 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8356 (tm-30) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 1.5716 time to fit residues: 94.9403 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.090038 restraints weight = 4227.280| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.55 r_work: 0.2750 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3386 Z= 0.128 Angle : 0.436 4.438 4598 Z= 0.230 Chirality : 0.041 0.127 501 Planarity : 0.005 0.047 586 Dihedral : 5.729 76.191 462 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 15.34 % Favored : 83.48 % 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: 1.28 (0.42), residues: 414 helix: 2.28 (0.35), residues: 207 sheet: 0.09 (0.66), residues: 73 loop : -1.01 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.009 0.001 ARG A 265 *********************** 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 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.342 Fit side-chains REVERT: A 21 MET cc_start: 0.8934 (ptm) cc_final: 0.8694 (ptt) REVERT: A 29 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 246 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (mpt180) outliers start: 4 outliers final: 1 residues processed: 63 average time/residue: 1.5003 time to fit residues: 96.8127 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087363 restraints weight = 4146.301| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.52 r_work: 0.2716 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.154 Angle : 0.438 4.445 4598 Z= 0.232 Chirality : 0.041 0.128 501 Planarity : 0.005 0.047 586 Dihedral : 5.614 72.117 462 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 16.22 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.42), residues: 414 helix: 2.23 (0.35), residues: 208 sheet: 0.13 (0.66), residues: 73 loop : -0.94 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 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 0.009 0.000 ARG A 370 *********************** 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 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.392 Fit side-chains REVERT: A 21 MET cc_start: 0.8959 (ptm) cc_final: 0.8702 (ptt) REVERT: A 29 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 282 GLU cc_start: 0.8517 (mp0) cc_final: 0.8158 (mp0) REVERT: A 332 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8455 (tm-30) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 1.5134 time to fit residues: 99.2254 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER 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 37 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.112311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.087869 restraints weight = 4149.378| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.52 r_work: 0.2731 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.151 Angle : 0.439 4.436 4598 Z= 0.233 Chirality : 0.041 0.128 501 Planarity : 0.004 0.047 586 Dihedral : 5.406 66.421 462 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 16.22 % Favored : 82.89 % 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: 1.33 (0.42), residues: 414 helix: 2.27 (0.35), residues: 207 sheet: 0.13 (0.66), residues: 73 loop : -0.92 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.008 0.000 ARG A 370 *********************** 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 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.437 Fit side-chains REVERT: A 21 MET cc_start: 0.8945 (ptm) cc_final: 0.8681 (ptt) REVERT: A 29 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8642 (mm-30) REVERT: A 282 GLU cc_start: 0.8521 (mp0) cc_final: 0.8169 (mp0) REVERT: A 332 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8462 (tm-30) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 1.6586 time to fit residues: 110.2890 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.113923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.089518 restraints weight = 4154.452| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.54 r_work: 0.2743 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.140 Angle : 0.439 4.584 4598 Z= 0.232 Chirality : 0.041 0.126 501 Planarity : 0.005 0.047 586 Dihedral : 5.030 56.467 462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.59 % Allowed : 16.52 % Favored : 82.89 % 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: 1.42 (0.42), residues: 414 helix: 2.33 (0.35), residues: 207 sheet: 0.21 (0.66), residues: 73 loop : -0.86 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.010 0.001 ARG A 265 *********************** 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 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.379 Fit side-chains REVERT: A 21 MET cc_start: 0.8924 (ptm) cc_final: 0.8660 (ptt) REVERT: A 29 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8720 (mm-30) REVERT: A 282 GLU cc_start: 0.8508 (mp0) cc_final: 0.8197 (mp0) REVERT: A 332 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8464 (tm-30) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 1.4533 time to fit residues: 93.8396 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.110751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.086485 restraints weight = 4153.943| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.51 r_work: 0.2713 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3386 Z= 0.196 Angle : 0.476 5.229 4598 Z= 0.253 Chirality : 0.042 0.130 501 Planarity : 0.005 0.048 586 Dihedral : 4.990 50.252 462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 16.52 % Favored : 82.30 % 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: 1.34 (0.42), residues: 414 helix: 2.21 (0.35), residues: 208 sheet: 0.17 (0.66), residues: 73 loop : -0.85 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.012 0.001 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.009 0.001 ARG A 265 ********************** 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 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.380 Fit side-chains REVERT: A 21 MET cc_start: 0.8980 (ptm) cc_final: 0.8752 (ptt) REVERT: A 29 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 282 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 332 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8465 (tm-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.5408 time to fit residues: 100.9674 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.088565 restraints weight = 4161.301| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.54 r_work: 0.2758 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.141 Angle : 0.443 5.770 4598 Z= 0.233 Chirality : 0.041 0.128 501 Planarity : 0.004 0.047 586 Dihedral : 4.593 40.542 462 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.88 % Allowed : 17.11 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.42), residues: 414 helix: 2.33 (0.35), residues: 207 sheet: 0.30 (0.67), residues: 73 loop : -0.84 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.66 seconds wall clock time: 52 minutes 0.80 seconds (3120.80 seconds total)