Starting phenix.real_space_refine on Wed Mar 5 22:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjg_37579/03_2025/8wjg_37579.cif" } resolution = 3.0 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= 0.004 sd= 0.167 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2569 2.51 5 N 672 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3952 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3952 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 29, 'TRANS': 503} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.02, per 1000 atoms: 0.76 Number of scatterers: 3952 At special positions: 0 Unit cell: (104.86, 85.6, 64.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 680 8.00 N 672 7.00 C 2569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 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: 1.07 Conformation dependent library (CDL) restraints added in 548.0 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 83.3% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.732A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 removed outlier: 4.754A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.776A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.550A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.829A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.922A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.785A pdb=" N ASP A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.742A pdb=" N LEU A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 removed outlier: 3.950A pdb=" N PHE A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.754A pdb=" N GLY A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.751A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 460 removed outlier: 3.889A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 490 removed outlier: 4.476A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.535A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 305 hydrogen bonds defined for protein. 882 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: 1.18 Time building geometry restraints manager: 1.26 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: 1252 1.34 - 1.47: 984 1.47 - 1.59: 1761 1.59 - 1.71: 0 1.71 - 1.84: 50 Bond restraints: 4047 Sorted by residual: bond pdb=" C MET A 36 " pdb=" O MET A 36 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.38e-02 5.25e+03 4.04e+00 bond pdb=" CG PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.503 1.438 0.065 3.40e-02 8.65e+02 3.64e+00 bond pdb=" N PRO A 194 " pdb=" CA PRO A 194 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.25e+00 bond pdb=" CB MET A 222 " pdb=" CG MET A 222 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 4042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 5385 3.17 - 6.34: 113 6.34 - 9.51: 17 9.51 - 12.68: 6 12.68 - 15.85: 5 Bond angle restraints: 5526 Sorted by residual: angle pdb=" CA PRO A 194 " pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 112.00 97.41 14.59 1.40e+00 5.10e-01 1.09e+02 angle pdb=" C ALA A 323 " pdb=" N MET A 324 " pdb=" CA MET A 324 " ideal model delta sigma weight residual 121.66 109.91 11.75 1.76e+00 3.23e-01 4.45e+01 angle pdb=" CB MET A 222 " pdb=" CG MET A 222 " pdb=" SD MET A 222 " ideal model delta sigma weight residual 112.70 97.37 15.33 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C THR A 518 " pdb=" N GLN A 519 " pdb=" CA GLN A 519 " ideal model delta sigma weight residual 125.66 134.53 -8.87 1.85e+00 2.92e-01 2.30e+01 angle pdb=" CB MET A 324 " pdb=" CG MET A 324 " pdb=" SD MET A 324 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 ... (remaining 5521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 2132 17.27 - 34.55: 160 34.55 - 51.82: 51 51.82 - 69.09: 19 69.09 - 86.36: 4 Dihedral angle restraints: 2366 sinusoidal: 849 harmonic: 1517 Sorted by residual: dihedral pdb=" CA GLY A 375 " pdb=" C GLY A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 135.06 -42.06 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " pdb=" NH1 ARG A 487 " ideal model delta sinusoidal sigma weight residual 0.00 -28.91 28.91 1 1.00e+01 1.00e-02 1.20e+01 ... (remaining 2363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 459 0.051 - 0.101: 135 0.101 - 0.152: 45 0.152 - 0.202: 12 0.202 - 0.252: 4 Chirality restraints: 655 Sorted by residual: chirality pdb=" CA MET A 466 " pdb=" N MET A 466 " pdb=" C MET A 466 " pdb=" CB MET A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 13 " pdb=" CB LEU A 13 " pdb=" CD1 LEU A 13 " pdb=" CD2 LEU A 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ARG A 89 " pdb=" N ARG A 89 " pdb=" C ARG A 89 " pdb=" CB ARG A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 652 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 193 " -0.143 5.00e-02 4.00e+02 2.05e-01 6.75e+01 pdb=" N PRO A 194 " 0.354 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 487 " -0.387 9.50e-02 1.11e+02 1.75e-01 2.36e+01 pdb=" NE ARG A 487 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 487 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 487 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 291 " 0.311 9.50e-02 1.11e+02 1.40e-01 1.49e+01 pdb=" NE ARG A 291 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 291 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 291 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 291 " 0.001 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 386 2.75 - 3.29: 4110 3.29 - 3.82: 6933 3.82 - 4.36: 7768 4.36 - 4.90: 13339 Nonbonded interactions: 32536 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" O PRO A 516 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 412 " pdb=" O GLY A 444 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASN A 216 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A 257 " pdb=" OG1 THR A 259 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 359 " pdb=" OG1 THR A 363 " model vdw 2.297 3.040 ... (remaining 32531 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: 0.380 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.750 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4047 Z= 0.334 Angle : 1.210 15.847 5526 Z= 0.659 Chirality : 0.059 0.252 655 Planarity : 0.014 0.205 691 Dihedral : 15.276 86.364 1382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 21.83 % Favored : 76.14 % 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: 0.84 (0.34), residues: 529 helix: 1.01 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.032 0.003 PHE A 208 TYR 0.030 0.008 TYR A 275 ARG 0.039 0.003 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.434 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.1892 time to fit residues: 79.0128 Evaluate side-chains 59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132931 restraints weight = 3941.702| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.05 r_work: 0.3598 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.210 Angle : 0.673 11.273 5526 Z= 0.327 Chirality : 0.041 0.134 655 Planarity : 0.006 0.095 691 Dihedral : 5.100 50.618 571 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.81 % Allowed : 20.81 % Favored : 75.38 % 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: 1.70 (0.38), residues: 529 helix: 1.64 (0.26), residues: 399 sheet: -1.07 (1.35), residues: 10 loop : -0.29 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.019 0.002 PHE A 208 TYR 0.017 0.003 TYR A 275 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.397 Fit side-chains REVERT: A 5 GLU cc_start: 0.6988 (mp0) cc_final: 0.6645 (mp0) REVERT: A 38 GLU cc_start: 0.8127 (tt0) cc_final: 0.7927 (tp30) REVERT: A 39 ASN cc_start: 0.8051 (t0) cc_final: 0.7813 (t0) REVERT: A 170 PHE cc_start: 0.8462 (m-80) cc_final: 0.8213 (m-80) REVERT: A 529 ASP cc_start: 0.6921 (t0) cc_final: 0.6679 (t0) outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 0.9844 time to fit residues: 82.1081 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.169872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129375 restraints weight = 4130.191| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.05 r_work: 0.3511 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4047 Z= 0.175 Angle : 0.635 9.707 5526 Z= 0.306 Chirality : 0.038 0.120 655 Planarity : 0.005 0.062 691 Dihedral : 4.874 57.018 569 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.79 % Allowed : 21.83 % Favored : 75.38 % 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: 2.09 (0.37), residues: 529 helix: 1.93 (0.26), residues: 387 sheet: -1.25 (1.34), residues: 10 loop : 0.06 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.020 0.002 PHE A 208 TYR 0.019 0.003 TYR A 275 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.391 Fit side-chains REVERT: A 5 GLU cc_start: 0.7130 (mp0) cc_final: 0.6792 (mp0) REVERT: A 38 GLU cc_start: 0.7953 (tt0) cc_final: 0.7639 (tp30) REVERT: A 114 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6478 (pp20) REVERT: A 297 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6722 (tp40) REVERT: A 430 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6481 (mmm) REVERT: A 529 ASP cc_start: 0.6970 (t0) cc_final: 0.6762 (t0) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 1.0204 time to fit residues: 76.4347 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124676 restraints weight = 4198.780| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.12 r_work: 0.3480 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4047 Z= 0.203 Angle : 0.624 7.346 5526 Z= 0.303 Chirality : 0.038 0.124 655 Planarity : 0.005 0.048 691 Dihedral : 4.879 59.563 569 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.79 % Allowed : 20.56 % Favored : 76.65 % 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: 1.95 (0.37), residues: 529 helix: 1.82 (0.26), residues: 395 sheet: -1.02 (1.37), residues: 10 loop : -0.11 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 294 HIS 0.005 0.001 HIS A 245 PHE 0.020 0.002 PHE A 208 TYR 0.019 0.002 TYR A 275 ARG 0.010 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.395 Fit side-chains REVERT: A 5 GLU cc_start: 0.7012 (mp0) cc_final: 0.6791 (mp0) REVERT: A 38 GLU cc_start: 0.7932 (tt0) cc_final: 0.7669 (tp30) REVERT: A 228 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8222 (ttp80) REVERT: A 297 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6802 (tp40) REVERT: A 430 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6522 (mmm) REVERT: A 466 MET cc_start: 0.8102 (mmm) cc_final: 0.7841 (mmm) REVERT: A 529 ASP cc_start: 0.7007 (t0) cc_final: 0.6799 (t0) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 1.0593 time to fit residues: 72.6089 Evaluate side-chains 56 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123804 restraints weight = 4333.668| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.09 r_work: 0.3438 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4047 Z= 0.197 Angle : 0.612 7.404 5526 Z= 0.298 Chirality : 0.038 0.122 655 Planarity : 0.004 0.037 691 Dihedral : 4.842 57.851 569 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.81 % Allowed : 20.56 % Favored : 75.63 % 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: 2.00 (0.37), residues: 529 helix: 1.87 (0.26), residues: 393 sheet: -1.35 (1.35), residues: 10 loop : -0.06 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.019 0.002 PHE A 208 TYR 0.019 0.002 TYR A 275 ARG 0.007 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.451 Fit side-chains REVERT: A 38 GLU cc_start: 0.7920 (tt0) cc_final: 0.7667 (tp30) REVERT: A 228 ARG cc_start: 0.8738 (ttp-110) cc_final: 0.8297 (ttp80) REVERT: A 297 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6822 (tp40) REVERT: A 300 TRP cc_start: 0.7039 (m-10) cc_final: 0.6803 (m100) REVERT: A 320 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6270 (tp) REVERT: A 369 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7522 (mt) REVERT: A 430 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6516 (mmm) REVERT: A 466 MET cc_start: 0.8098 (mmm) cc_final: 0.7834 (mmm) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 0.9298 time to fit residues: 72.7959 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124756 restraints weight = 4180.351| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.10 r_work: 0.3442 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4047 Z= 0.167 Angle : 0.594 9.049 5526 Z= 0.289 Chirality : 0.037 0.121 655 Planarity : 0.004 0.035 691 Dihedral : 4.710 54.475 569 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.55 % Allowed : 22.84 % Favored : 73.60 % 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: 2.14 (0.37), residues: 529 helix: 1.98 (0.26), residues: 393 sheet: -1.69 (1.38), residues: 10 loop : -0.03 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.022 0.002 PHE A 40 TYR 0.018 0.002 TYR A 275 ARG 0.007 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.365 Fit side-chains REVERT: A 5 GLU cc_start: 0.7618 (mp0) cc_final: 0.7163 (mp0) REVERT: A 38 GLU cc_start: 0.7674 (tt0) cc_final: 0.7421 (tp30) REVERT: A 228 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8200 (ttp80) REVERT: A 297 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6752 (tp40) REVERT: A 300 TRP cc_start: 0.7062 (m-10) cc_final: 0.6808 (m100) REVERT: A 364 PHE cc_start: 0.7423 (t80) cc_final: 0.7200 (t80) REVERT: A 369 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7395 (mt) outliers start: 14 outliers final: 6 residues processed: 70 average time/residue: 1.0613 time to fit residues: 77.1211 Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.165019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123560 restraints weight = 4191.341| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.09 r_work: 0.3419 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.186 Angle : 0.614 9.905 5526 Z= 0.295 Chirality : 0.038 0.132 655 Planarity : 0.004 0.035 691 Dihedral : 4.650 51.918 569 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.05 % Allowed : 24.37 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.37), residues: 529 helix: 1.95 (0.26), residues: 395 sheet: -1.72 (1.44), residues: 10 loop : -0.17 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.020 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.009 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.411 Fit side-chains REVERT: A 5 GLU cc_start: 0.7662 (mp0) cc_final: 0.7202 (mp0) REVERT: A 228 ARG cc_start: 0.8740 (ttp-110) cc_final: 0.8400 (ttp80) REVERT: A 297 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6743 (tp40) REVERT: A 300 TRP cc_start: 0.7147 (m-10) cc_final: 0.6872 (m100) REVERT: A 369 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7340 (mt) REVERT: A 529 ASP cc_start: 0.7018 (t0) cc_final: 0.6765 (t0) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.9198 time to fit residues: 67.2436 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123637 restraints weight = 4186.911| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.13 r_work: 0.3444 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4047 Z= 0.201 Angle : 0.629 10.559 5526 Z= 0.302 Chirality : 0.038 0.123 655 Planarity : 0.004 0.035 691 Dihedral : 4.603 48.662 569 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.55 % Allowed : 24.62 % Favored : 71.83 % 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: 2.04 (0.38), residues: 529 helix: 1.91 (0.26), residues: 396 sheet: -1.73 (1.44), residues: 10 loop : -0.13 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.019 0.002 PHE A 40 TYR 0.020 0.002 TYR A 275 ARG 0.007 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.420 Fit side-chains REVERT: A 5 GLU cc_start: 0.7773 (mp0) cc_final: 0.7291 (mp0) REVERT: A 228 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8430 (ttp80) REVERT: A 297 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6750 (tp40) REVERT: A 300 TRP cc_start: 0.7216 (m-10) cc_final: 0.6979 (m-10) REVERT: A 369 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7380 (mt) REVERT: A 452 ILE cc_start: 0.8422 (tp) cc_final: 0.8186 (OUTLIER) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 1.0668 time to fit residues: 78.5860 Evaluate side-chains 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121756 restraints weight = 4231.300| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.13 r_work: 0.3432 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4047 Z= 0.207 Angle : 0.643 11.260 5526 Z= 0.307 Chirality : 0.039 0.146 655 Planarity : 0.004 0.035 691 Dihedral : 4.544 44.559 569 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.79 % Allowed : 25.63 % Favored : 71.57 % 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: 1.96 (0.38), residues: 529 helix: 1.86 (0.26), residues: 396 sheet: -1.65 (1.45), residues: 10 loop : -0.18 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.019 0.002 PHE A 40 TYR 0.020 0.002 TYR A 275 ARG 0.007 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7861 (mp0) cc_final: 0.7300 (mp0) REVERT: A 114 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6406 (pp20) REVERT: A 228 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.8414 (ttp80) REVERT: A 297 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6725 (tp40) REVERT: A 300 TRP cc_start: 0.7290 (m-10) cc_final: 0.7068 (m-10) REVERT: A 369 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7081 (mt) REVERT: A 452 ILE cc_start: 0.8433 (tp) cc_final: 0.8192 (OUTLIER) REVERT: A 529 ASP cc_start: 0.7064 (t0) cc_final: 0.6813 (t0) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 1.1598 time to fit residues: 93.9108 Evaluate side-chains 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.165145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123677 restraints weight = 4171.955| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.10 r_work: 0.3429 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.178 Angle : 0.641 11.893 5526 Z= 0.304 Chirality : 0.038 0.118 655 Planarity : 0.004 0.034 691 Dihedral : 4.429 39.382 569 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.79 % Allowed : 25.89 % Favored : 71.32 % 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: 1.99 (0.38), residues: 529 helix: 1.88 (0.26), residues: 397 sheet: -1.79 (1.51), residues: 10 loop : -0.18 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.008 0.001 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7828 (mp0) cc_final: 0.7233 (mp0) REVERT: A 88 CYS cc_start: 0.6751 (m) cc_final: 0.6385 (m) REVERT: A 114 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: A 228 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8401 (ttp80) REVERT: A 297 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6726 (tp40) REVERT: A 300 TRP cc_start: 0.7309 (m-10) cc_final: 0.7071 (m100) REVERT: A 369 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7196 (mt) REVERT: A 452 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (OUTLIER) REVERT: A 495 TRP cc_start: 0.6617 (p-90) cc_final: 0.6158 (p90) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 1.0586 time to fit residues: 80.5494 Evaluate side-chains 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.165719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124424 restraints weight = 4186.821| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.09 r_work: 0.3491 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4047 Z= 0.180 Angle : 0.642 11.467 5526 Z= 0.304 Chirality : 0.038 0.120 655 Planarity : 0.004 0.034 691 Dihedral : 4.320 34.544 569 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.54 % Allowed : 25.89 % Favored : 71.57 % 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: 1.99 (0.38), residues: 529 helix: 1.90 (0.26), residues: 397 sheet: -1.66 (1.47), residues: 10 loop : -0.27 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 208 TYR 0.019 0.002 TYR A 275 ARG 0.008 0.001 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5380.22 seconds wall clock time: 92 minutes 2.73 seconds (5522.73 seconds total)