Starting phenix.real_space_refine on Mon Jan 13 17:03:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znd_60268/01_2025/8znd_60268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znd_60268/01_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_60268/01_2025/8znd_60268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znd_60268/01_2025/8znd_60268.map" model { file = "/net/cci-nas-00/data/ceres_data/8znd_60268/01_2025/8znd_60268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znd_60268/01_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-5571/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: 2.90, per 1000 atoms: 0.87 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: 0.92 Conformation dependent library (CDL) restraints added in 423.7 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: 0.38 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: 1.04 Time building geometry restraints manager: 0.97 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.410 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- 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 : 0.402 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 1.5991 time to fit residues: 137.3803 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 : 0.397 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.114727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089924 restraints weight = 4071.699| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.52 r_work: 0.2770 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1817 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= 0.162 Angle : 0.467 4.374 4598 Z= 0.249 Chirality : 0.042 0.132 501 Planarity : 0.005 0.044 586 Dihedral : 6.588 101.702 462 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 11.50 % 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: 1.11 (0.42), residues: 414 helix: 2.01 (0.35), residues: 209 sheet: 0.06 (0.65), residues: 72 loop : -0.93 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.004 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 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.376 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 1.5514 time to fit residues: 111.4015 Evaluate side-chains 60 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.110677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.085405 restraints weight = 4071.525| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.55 r_work: 0.2680 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3386 Z= 0.198 Angle : 0.471 4.473 4598 Z= 0.251 Chirality : 0.042 0.130 501 Planarity : 0.005 0.046 586 Dihedral : 6.362 89.487 462 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.29 % Allowed : 13.57 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.43), residues: 414 helix: 2.07 (0.35), residues: 209 sheet: 0.17 (0.65), residues: 72 loop : -0.92 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.008 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 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.371 Fit side-chains REVERT: A 21 MET cc_start: 0.8845 (ptm) cc_final: 0.8587 (ptt) REVERT: A 246 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8256 (mpt180) REVERT: A 265 ARG cc_start: 0.8413 (mmt90) cc_final: 0.8095 (mpp80) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.6763 time to fit residues: 102.9455 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.107836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.082671 restraints weight = 4124.986| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.55 r_work: 0.2638 rms_B_bonded: 1.89 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: 0.9032 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3386 Z= 0.413 Angle : 0.572 4.784 4598 Z= 0.306 Chirality : 0.048 0.133 501 Planarity : 0.006 0.077 586 Dihedral : 6.592 87.729 462 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.36 % Allowed : 12.39 % Favored : 85.25 % 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: 1.81 (0.35), residues: 209 sheet: -0.06 (0.63), residues: 72 loop : -0.97 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.019 0.002 TYR A 363 ARG 0.004 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 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.367 Fit side-chains REVERT: A 246 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8395 (mpt180) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 1.6264 time to fit residues: 96.5113 Evaluate side-chains 60 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.113678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.088841 restraints weight = 4167.749| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.56 r_work: 0.2731 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.129 Angle : 0.432 4.368 4598 Z= 0.229 Chirality : 0.041 0.127 501 Planarity : 0.004 0.046 586 Dihedral : 5.992 81.396 462 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.47 % Allowed : 14.45 % Favored : 84.07 % 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: 1.24 (0.42), residues: 414 helix: 2.19 (0.35), residues: 208 sheet: 0.08 (0.65), residues: 73 loop : -0.94 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.005 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.367 Fit side-chains REVERT: A 29 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8739 (mm-30) REVERT: A 265 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8157 (mmt90) outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 1.5800 time to fit residues: 101.8696 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.112708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.087929 restraints weight = 4158.900| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.57 r_work: 0.2699 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3386 Z= 0.152 Angle : 0.446 4.409 4598 Z= 0.235 Chirality : 0.041 0.129 501 Planarity : 0.004 0.047 586 Dihedral : 5.767 76.555 462 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 : 1.77 % Allowed : 15.04 % Favored : 83.19 % 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: 1.35 (0.43), residues: 414 helix: 2.23 (0.35), residues: 209 sheet: 0.19 (0.66), residues: 73 loop : -0.87 (0.55), residues: 132 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 0.012 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 ARG A 370 *********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.395 Fit side-chains REVERT: A 29 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8685 (mm-30) REVERT: A 265 ARG cc_start: 0.8427 (mtt90) cc_final: 0.8198 (mmt90) REVERT: A 332 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8432 (tm-30) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 1.6376 time to fit residues: 105.5807 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 : 0.419 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.111929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087158 restraints weight = 4094.659| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.55 r_work: 0.2693 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3386 Z= 0.169 Angle : 0.450 4.463 4598 Z= 0.237 Chirality : 0.042 0.130 501 Planarity : 0.004 0.047 586 Dihedral : 5.667 72.897 462 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 15.34 % Favored : 83.19 % 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: 209 sheet: 0.14 (0.66), residues: 73 loop : -0.82 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.006 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 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.423 Fit side-chains REVERT: A 29 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8665 (mm-30) REVERT: A 265 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8219 (mmt90) REVERT: A 282 GLU cc_start: 0.8526 (mp0) cc_final: 0.8197 (mp0) REVERT: A 332 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8426 (tm-30) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 1.6526 time to fit residues: 106.5756 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 8.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.112461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.087753 restraints weight = 4103.593| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.54 r_work: 0.2715 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2864 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= 0.155 Angle : 0.446 4.468 4598 Z= 0.235 Chirality : 0.041 0.129 501 Planarity : 0.004 0.047 586 Dihedral : 5.467 68.202 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 15.04 % 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: 1.42 (0.42), residues: 414 helix: 2.25 (0.35), residues: 209 sheet: 0.20 (0.66), residues: 73 loop : -0.76 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.007 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: 5 poor density : 61 time to evaluate : 0.386 Fit side-chains REVERT: A 29 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8690 (mm-30) REVERT: A 265 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8238 (mmt90) REVERT: A 282 GLU cc_start: 0.8513 (mp0) cc_final: 0.8234 (mp0) REVERT: A 332 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8452 (tm-30) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 1.6506 time to fit residues: 109.8716 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 : 0.403 ------------------------------------------------------------------------------- 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: 0.3980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 19 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.114681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.090170 restraints weight = 4141.402| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.57 r_work: 0.2801 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2983 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= 0.125 Angle : 0.427 4.635 4598 Z= 0.224 Chirality : 0.041 0.126 501 Planarity : 0.004 0.047 586 Dihedral : 4.975 57.124 462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 15.63 % Favored : 83.19 % 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: 1.58 (0.43), residues: 414 helix: 2.39 (0.35), residues: 208 sheet: 0.31 (0.66), residues: 73 loop : -0.70 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.007 0.000 ARG A 370 *********************** 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 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.379 Fit side-chains REVERT: A 29 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 282 GLU cc_start: 0.8498 (mp0) cc_final: 0.8219 (mp0) REVERT: A 332 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8472 (tm-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.6502 time to fit residues: 108.1769 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.110033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.085384 restraints weight = 4067.293| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.52 r_work: 0.2668 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3386 Z= 0.233 Angle : 0.499 5.104 4598 Z= 0.264 Chirality : 0.043 0.131 501 Planarity : 0.005 0.048 586 Dihedral : 5.107 52.637 462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 16.22 % Favored : 82.60 % 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: 2.12 (0.35), residues: 209 sheet: 0.29 (0.66), residues: 72 loop : -0.76 (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 0.013 0.002 PHE A 341 TYR 0.014 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.392 Fit side-chains REVERT: A 29 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8716 (mm-30) REVERT: A 282 GLU cc_start: 0.8573 (mp0) cc_final: 0.8288 (mp0) REVERT: A 332 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8454 (tm-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.6823 time to fit residues: 110.1705 Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.113343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.088832 restraints weight = 4084.295| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.53 r_work: 0.2734 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2947 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= 0.136 Angle : 0.446 5.758 4598 Z= 0.234 Chirality : 0.041 0.127 501 Planarity : 0.004 0.047 586 Dihedral : 4.618 42.191 462 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 16.81 % 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: 1.51 (0.43), residues: 414 helix: 2.35 (0.35), residues: 207 sheet: 0.29 (0.66), residues: 73 loop : -0.76 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.007 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.34 seconds wall clock time: 55 minutes 34.06 seconds (3334.06 seconds total)