Starting phenix.real_space_refine on Wed Mar 5 20:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.map" model { file = "/net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xco_38249/03_2025/8xco_38249.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 565 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3335 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3321 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 62 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 14} Link IDs: {None: 14} Time building chain proxies: 4.33, per 1000 atoms: 1.30 Number of scatterers: 3335 At special positions: 0 Unit cell: (69.936, 68.432, 73.696, 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 638 8.00 N 565 7.00 C 2115 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: 0.79 Conformation dependent library (CDL) restraints added in 787.2 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 54.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.525A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.958A 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 164 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.503A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 323 through 333 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 removed outlier: 3.520A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.421A 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: 4.691A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.911A 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: 6.405A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 569 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: 0.99 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1068 1.34 - 1.46: 583 1.46 - 1.57: 1720 1.57 - 1.69: 3 1.69 - 1.80: 27 Bond restraints: 3401 Sorted by residual: bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.29e-02 6.01e+03 5.12e+01 bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C GLY A 183 " pdb=" N SER A 184 " ideal model delta sigma weight residual 1.331 1.436 -0.105 1.51e-02 4.39e+03 4.85e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 4580 4.41 - 8.82: 25 8.82 - 13.24: 13 13.24 - 17.65: 4 17.65 - 22.06: 1 Bond angle restraints: 4623 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.47 -22.06 2.71e+00 1.37e-01 6.65e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.18 -15.34 1.91e+00 2.73e-01 6.42e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.34 -14.60 1.95e+00 2.62e-01 5.58e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.47 7.99 1.17e+00 7.36e-01 4.69e+01 angle pdb=" O2X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.33 108.95 8.38 1.48e+00 4.57e-01 3.21e+01 ... (remaining 4618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 1835 23.83 - 47.67: 137 47.67 - 71.50: 36 71.50 - 95.34: 4 95.34 - 119.17: 1 Dihedral angle restraints: 2013 sinusoidal: 820 harmonic: 1193 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 55.87 119.17 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " pdb=" OD1 ASP A 256 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " pdb=" OD1 ASN A 319 " ideal model delta sinusoidal sigma weight residual -90.00 -159.73 69.73 2 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 433 0.079 - 0.158: 59 0.158 - 0.236: 4 0.236 - 0.315: 3 0.315 - 0.394: 3 Chirality restraints: 502 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 -2.32 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.36 2.00e-01 2.50e+01 3.32e+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 2.24 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 499 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.92e+02 pdb=" C5N NDP A 500 " 0.256 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.26e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 144 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.050 5.00e-02 4.00e+02 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1329 2.92 - 3.41: 3324 3.41 - 3.91: 5836 3.91 - 4.40: 6734 4.40 - 4.90: 11087 Nonbonded interactions: 28310 Sorted by model distance: nonbonded pdb=" OH TYR A 352 " pdb=" O HOH A 601 " model vdw 2.424 3.040 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 602 " model vdw 2.446 3.120 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.505 3.120 nonbonded pdb=" OD2 ASP A 47 " pdb=" OG SER A 116 " model vdw 2.516 3.040 nonbonded pdb=" O2B NDP A 500 " pdb=" O3B NDP A 500 " model vdw 2.532 2.432 ... (remaining 28305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.250 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.420 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.009 0.264 3401 Z= 0.586 Angle : 1.129 22.060 4623 Z= 0.602 Chirality : 0.060 0.394 502 Planarity : 0.011 0.198 587 Dihedral : 17.486 119.173 1253 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.78 % Allowed : 4.72 % Favored : 88.50 % 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: 0.92 (0.42), residues: 415 helix: 1.60 (0.35), residues: 211 sheet: -0.20 (0.69), residues: 66 loop : -0.44 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.001 0.000 HIS A 75 PHE 0.010 0.001 PHE A 341 TYR 0.004 0.001 TYR A 101 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.372 Fit side-chains REVERT: A 149 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8638 (p0) REVERT: A 263 TRP cc_start: 0.8650 (t-100) cc_final: 0.8322 (t-100) REVERT: A 310 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8028 (mttp) outliers start: 23 outliers final: 1 residues processed: 105 average time/residue: 1.3140 time to fit residues: 141.6679 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 310 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 337 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.077032 restraints weight = 10224.348| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.44 r_work: 0.2639 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.168 Angle : 0.496 6.568 4623 Z= 0.255 Chirality : 0.042 0.148 502 Planarity : 0.005 0.071 587 Dihedral : 7.691 121.164 471 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.95 % Allowed : 17.11 % Favored : 79.94 % 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: 1.77 (0.44), residues: 415 helix: 2.26 (0.36), residues: 213 sheet: 0.36 (0.76), residues: 58 loop : -0.09 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 250 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.414 Fit side-chains REVERT: A 262 LYS cc_start: 0.8644 (tttp) cc_final: 0.8349 (tttm) REVERT: A 263 TRP cc_start: 0.8805 (t-100) cc_final: 0.8512 (t-100) REVERT: A 266 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8447 (mt-10) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 1.4522 time to fit residues: 96.9687 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 243 SER 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: 5.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.074742 restraints weight = 4326.209| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.56 r_work: 0.2624 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3401 Z= 0.209 Angle : 0.488 5.290 4623 Z= 0.257 Chirality : 0.043 0.151 502 Planarity : 0.005 0.059 587 Dihedral : 6.636 98.323 466 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 17.40 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.43), residues: 415 helix: 2.25 (0.35), residues: 213 sheet: 0.25 (0.70), residues: 70 loop : -0.02 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 364 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.399 Fit side-chains REVERT: A 243 SER cc_start: 0.8424 (t) cc_final: 0.8224 (p) REVERT: A 263 TRP cc_start: 0.8786 (t-100) cc_final: 0.8537 (t-100) REVERT: A 312 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8524 (mtpt) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 1.3038 time to fit residues: 77.9289 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.072872 restraints weight = 13821.186| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.78 r_work: 0.2547 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3401 Z= 0.180 Angle : 0.463 5.296 4623 Z= 0.242 Chirality : 0.043 0.138 502 Planarity : 0.005 0.054 587 Dihedral : 6.115 80.597 466 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 18.88 % Favored : 79.65 % 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: 1.80 (0.43), residues: 415 helix: 2.35 (0.35), residues: 213 sheet: 0.08 (0.69), residues: 72 loop : -0.03 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 364 HIS 0.001 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.363 Fit side-chains REVERT: A 78 GLU cc_start: 0.8500 (tp30) cc_final: 0.8245 (mm-30) REVERT: A 243 SER cc_start: 0.8494 (t) cc_final: 0.8284 (p) REVERT: A 263 TRP cc_start: 0.8813 (t-100) cc_final: 0.8556 (t-100) REVERT: A 392 ASN cc_start: 0.8923 (t0) cc_final: 0.8378 (t0) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 1.1939 time to fit residues: 73.7908 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.073344 restraints weight = 6191.017| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.87 r_work: 0.2592 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.213 Angle : 0.484 5.394 4623 Z= 0.254 Chirality : 0.043 0.142 502 Planarity : 0.005 0.051 587 Dihedral : 6.021 76.476 466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 16.81 % Favored : 80.53 % 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: 1.75 (0.43), residues: 415 helix: 2.32 (0.35), residues: 213 sheet: 0.07 (0.69), residues: 72 loop : -0.08 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.395 Fit side-chains REVERT: A 149 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8658 (p0) REVERT: A 243 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 263 TRP cc_start: 0.8767 (t-100) cc_final: 0.8535 (t-100) REVERT: A 392 ASN cc_start: 0.8937 (t0) cc_final: 0.8407 (t0) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 1.1569 time to fit residues: 68.1216 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.077201 restraints weight = 6639.758| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.93 r_work: 0.2659 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3401 Z= 0.129 Angle : 0.441 5.568 4623 Z= 0.230 Chirality : 0.041 0.126 502 Planarity : 0.004 0.047 587 Dihedral : 5.600 66.553 466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.59 % Allowed : 18.29 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.43), residues: 415 helix: 2.52 (0.35), residues: 213 sheet: 0.07 (0.68), residues: 72 loop : -0.12 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 250 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.395 Fit side-chains REVERT: A 78 GLU cc_start: 0.8346 (tp30) cc_final: 0.8102 (mm-30) REVERT: A 243 SER cc_start: 0.8512 (t) cc_final: 0.8287 (p) REVERT: A 263 TRP cc_start: 0.8748 (t-100) cc_final: 0.8505 (t-100) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 1.1940 time to fit residues: 69.0126 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.075435 restraints weight = 10222.746| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.41 r_work: 0.2605 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3401 Z= 0.145 Angle : 0.450 6.323 4623 Z= 0.235 Chirality : 0.042 0.126 502 Planarity : 0.004 0.047 587 Dihedral : 5.172 54.889 466 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.59 % Allowed : 18.88 % Favored : 80.53 % 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: 1.95 (0.43), residues: 415 helix: 2.54 (0.35), residues: 213 sheet: 0.18 (0.68), residues: 72 loop : -0.11 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: A 78 GLU cc_start: 0.8407 (tp30) cc_final: 0.8139 (mm-30) REVERT: A 149 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8494 (p0) REVERT: A 243 SER cc_start: 0.8524 (t) cc_final: 0.8306 (p) REVERT: A 263 TRP cc_start: 0.8755 (t-100) cc_final: 0.8514 (t-100) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 1.1939 time to fit residues: 67.8059 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.0770 chunk 29 optimal weight: 0.0870 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.111439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.080029 restraints weight = 6175.272| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.85 r_work: 0.2698 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3401 Z= 0.123 Angle : 0.438 6.493 4623 Z= 0.227 Chirality : 0.041 0.124 502 Planarity : 0.004 0.046 587 Dihedral : 4.730 45.419 466 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 17.70 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.43), residues: 415 helix: 2.65 (0.35), residues: 212 sheet: 0.22 (0.69), residues: 70 loop : -0.07 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.005 0.001 TYR A 160 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.386 Fit side-chains REVERT: A 78 GLU cc_start: 0.8346 (tp30) cc_final: 0.8109 (mm-30) REVERT: A 243 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 263 TRP cc_start: 0.8759 (t-100) cc_final: 0.8524 (t-100) REVERT: A 298 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 312 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8435 (mtpt) outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 1.2525 time to fit residues: 73.5353 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.075925 restraints weight = 7565.925| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.06 r_work: 0.2621 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3401 Z= 0.170 Angle : 0.470 7.011 4623 Z= 0.244 Chirality : 0.042 0.129 502 Planarity : 0.004 0.047 587 Dihedral : 4.553 45.181 464 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.29 % Allowed : 19.47 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.43), residues: 415 helix: 2.60 (0.35), residues: 212 sheet: 0.20 (0.68), residues: 72 loop : -0.02 (0.58), residues: 131 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 0.008 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.362 Fit side-chains REVERT: A 78 GLU cc_start: 0.8390 (tp30) cc_final: 0.8140 (mm-30) REVERT: A 263 TRP cc_start: 0.8751 (t-100) cc_final: 0.8528 (t-100) REVERT: A 312 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8446 (mtpt) REVERT: A 392 ASN cc_start: 0.8952 (t0) cc_final: 0.8411 (t0) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 1.1493 time to fit residues: 62.9453 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.077119 restraints weight = 6190.864| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.85 r_work: 0.2653 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3401 Z= 0.149 Angle : 0.463 7.242 4623 Z= 0.240 Chirality : 0.042 0.123 502 Planarity : 0.004 0.047 587 Dihedral : 4.463 43.795 464 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.88 % Allowed : 19.17 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 415 helix: 2.60 (0.35), residues: 212 sheet: 0.21 (0.68), residues: 72 loop : -0.07 (0.58), residues: 131 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 0.009 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.406 Fit side-chains REVERT: A 78 GLU cc_start: 0.8348 (tp30) cc_final: 0.8100 (mm-30) REVERT: A 263 TRP cc_start: 0.8746 (t-100) cc_final: 0.8528 (t-100) REVERT: A 312 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8421 (mtpt) REVERT: A 392 ASN cc_start: 0.8930 (t0) cc_final: 0.8396 (t0) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 1.1314 time to fit residues: 60.8891 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.074764 restraints weight = 11071.721| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.50 r_work: 0.2575 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.165 Angle : 0.468 7.178 4623 Z= 0.243 Chirality : 0.042 0.127 502 Planarity : 0.004 0.047 587 Dihedral : 4.440 42.803 464 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.18 % Allowed : 18.58 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.43), residues: 415 helix: 2.58 (0.35), residues: 212 sheet: 0.20 (0.68), residues: 72 loop : -0.03 (0.58), residues: 131 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 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3337.96 seconds wall clock time: 57 minutes 33.95 seconds (3453.95 seconds total)