Starting phenix.real_space_refine on Mon Feb 10 22:43:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.map" model { file = "/net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d69_46590/02_2025/9d69_46590.cif" } resolution = 2.99 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= 0.006 sd= 0.142 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: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 S 22 5.16 5 Na 3 4.78 5 C 2055 2.51 5 N 500 2.21 5 O 562 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-5592/modules/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3132 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 30.766 23.748 24.903 1.00 69.67 S Time building chain proxies: 2.93, per 1000 atoms: 0.93 Number of scatterers: 3143 At special positions: 0 Unit cell: (59.4, 69.3, 77.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 S 22 16.00 Na 3 11.00 O 562 8.00 N 500 7.00 C 2055 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: 0.93 Conformation dependent library (CDL) restraints added in 416.3 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 86.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.517A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.734A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 4.257A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.641A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.832A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.662A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.601A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.510A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.644A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.861A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.337A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 466 removed outlier: 4.002A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 removed outlier: 4.025A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 249 hydrogen bonds defined for protein. 744 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: 0.91 Time building geometry restraints manager: 0.96 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: 938 1.34 - 1.45: 359 1.45 - 1.57: 1847 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3184 Sorted by residual: bond pdb=" N GLN A 413 " pdb=" CA GLN A 413 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.32e-02 5.74e+03 5.42e+00 bond pdb=" N ARG A 342 " pdb=" CA ARG A 342 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.72e+00 bond pdb=" N ALA A 414 " pdb=" CA ALA A 414 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 3.00e+00 bond pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 1.233 1.216 0.017 1.19e-02 7.06e+03 2.01e+00 ... (remaining 3179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 4228 1.55 - 3.10: 68 3.10 - 4.64: 20 4.64 - 6.19: 4 6.19 - 7.74: 1 Bond angle restraints: 4321 Sorted by residual: angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.56 118.09 3.47 1.16e+00 7.43e-01 8.94e+00 angle pdb=" CA ARG A 342 " pdb=" C ARG A 342 " pdb=" O ARG A 342 " ideal model delta sigma weight residual 120.82 118.10 2.72 1.05e+00 9.07e-01 6.72e+00 angle pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " ideal model delta sigma weight residual 112.70 120.44 -7.74 3.00e+00 1.11e-01 6.66e+00 angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 111.71 108.77 2.94 1.15e+00 7.56e-01 6.52e+00 angle pdb=" CA MET A 255 " pdb=" CB MET A 255 " pdb=" CG MET A 255 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.66e+00 ... (remaining 4316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 1716 17.66 - 35.32: 127 35.32 - 52.97: 45 52.97 - 70.63: 10 70.63 - 88.29: 6 Dihedral angle restraints: 1904 sinusoidal: 721 harmonic: 1183 Sorted by residual: dihedral pdb=" CB GLU A 345 " pdb=" CG GLU A 345 " pdb=" CD GLU A 345 " pdb=" OE1 GLU A 345 " ideal model delta sinusoidal sigma weight residual 0.00 -88.29 88.29 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 469 " pdb=" CG GLU A 469 " pdb=" CD GLU A 469 " pdb=" OE1 GLU A 469 " ideal model delta sinusoidal sigma weight residual 0.00 -87.68 87.68 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB MET A 449 " pdb=" CG MET A 449 " pdb=" SD MET A 449 " pdb=" CE MET A 449 " ideal model delta sinusoidal sigma weight residual 60.00 119.52 -59.52 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 306 0.022 - 0.044: 126 0.044 - 0.067: 73 0.067 - 0.089: 36 0.089 - 0.111: 8 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.08e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 546 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 445 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.64e+00 pdb=" NE ARG A 445 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 445 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 445 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 445 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 342 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.29e+00 pdb=" NE ARG A 342 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 342 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 302 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.015 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 48 2.66 - 3.22: 3322 3.22 - 3.78: 4828 3.78 - 4.34: 6992 4.34 - 4.90: 11326 Nonbonded interactions: 26516 Sorted by model distance: nonbonded pdb=" O SER A 405 " pdb="NA NA A 602 " model vdw 2.096 2.470 nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.101 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.108 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.144 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.156 2.470 ... (remaining 26511 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.040 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.003 0.048 3184 Z= 0.195 Angle : 0.549 7.740 4321 Z= 0.291 Chirality : 0.035 0.111 549 Planarity : 0.008 0.116 527 Dihedral : 15.992 88.291 1140 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % 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: 0.78 (0.42), residues: 406 helix: 1.02 (0.30), residues: 318 sheet: -1.66 (1.10), residues: 18 loop : -0.87 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 373 ARG 0.022 0.001 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.8148 time to fit residues: 45.1080 Evaluate side-chains 44 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135284 restraints weight = 1349.323| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.15 r_work: 0.3406 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3184 Z= 0.247 Angle : 0.560 8.372 4321 Z= 0.297 Chirality : 0.039 0.134 549 Planarity : 0.004 0.025 527 Dihedral : 3.622 12.751 433 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.36 % Allowed : 17.15 % Favored : 78.49 % 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 (0.41), residues: 406 helix: 1.54 (0.28), residues: 325 sheet: -1.49 (1.08), residues: 18 loop : 0.07 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.002 PHE A 341 TYR 0.012 0.002 TYR A 97 ARG 0.003 0.001 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.339 Fit side-chains REVERT: A 252 GLN cc_start: 0.7875 (mt0) cc_final: 0.7661 (mt0) REVERT: A 290 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7607 (mm) REVERT: A 329 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6102 (mpm) REVERT: A 445 ARG cc_start: 0.7428 (mpt180) cc_final: 0.7060 (mpt-90) REVERT: A 468 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7847 (mttt) outliers start: 15 outliers final: 5 residues processed: 64 average time/residue: 1.0175 time to fit residues: 67.4285 Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.188275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140465 restraints weight = 1397.325| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.18 r_work: 0.3399 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3184 Z= 0.187 Angle : 0.494 5.682 4321 Z= 0.262 Chirality : 0.038 0.132 549 Planarity : 0.003 0.023 527 Dihedral : 3.580 16.050 433 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.78 % Allowed : 16.57 % 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: 2.00 (0.41), residues: 406 helix: 1.77 (0.28), residues: 324 sheet: -1.11 (1.10), residues: 18 loop : -0.05 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.010 0.002 TYR A 285 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.374 Fit side-chains REVERT: A 290 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 310 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7142 (tpp80) REVERT: A 342 ARG cc_start: 0.6496 (ttp-110) cc_final: 0.6005 (mtm110) REVERT: A 445 ARG cc_start: 0.7175 (mpt180) cc_final: 0.6740 (mpt-90) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 1.0026 time to fit residues: 65.4267 Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.189362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141559 restraints weight = 1455.713| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.20 r_work: 0.3438 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3184 Z= 0.191 Angle : 0.489 5.506 4321 Z= 0.259 Chirality : 0.038 0.133 549 Planarity : 0.003 0.023 527 Dihedral : 3.614 20.285 433 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 19.19 % Favored : 77.33 % 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 (0.41), residues: 406 helix: 1.81 (0.28), residues: 326 sheet: -1.19 (1.13), residues: 18 loop : -0.26 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 19 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.011 0.001 TYR A 285 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.360 Fit side-chains REVERT: A 290 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 297 SER cc_start: 0.8945 (m) cc_final: 0.8741 (p) REVERT: A 310 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7194 (tpp80) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 0.8416 time to fit residues: 56.1642 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.0270 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4113 r_free = 0.4113 target = 0.194082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146867 restraints weight = 1474.796| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.21 r_work: 0.3431 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3184 Z= 0.184 Angle : 0.484 5.138 4321 Z= 0.255 Chirality : 0.038 0.134 549 Planarity : 0.003 0.023 527 Dihedral : 3.597 22.448 433 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.91 % Allowed : 21.22 % Favored : 75.87 % 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: 2.22 (0.41), residues: 406 helix: 1.91 (0.28), residues: 326 sheet: -1.10 (1.13), residues: 18 loop : 0.05 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.010 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.360 Fit side-chains REVERT: A 286 MET cc_start: 0.7271 (mtp) cc_final: 0.6953 (mtp) REVERT: A 290 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 310 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7212 (tpp80) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.8353 time to fit residues: 51.4088 Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4005 r_free = 0.4005 target = 0.184682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134765 restraints weight = 1522.068| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.23 r_work: 0.3380 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3184 Z= 0.312 Angle : 0.560 6.240 4321 Z= 0.292 Chirality : 0.040 0.136 549 Planarity : 0.004 0.026 527 Dihedral : 3.855 28.580 433 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.36 % Allowed : 20.64 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.40), residues: 406 helix: 1.67 (0.28), residues: 326 sheet: -1.39 (1.11), residues: 18 loop : -0.11 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.018 0.002 PHE A 240 TYR 0.010 0.002 TYR A 285 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.274 Fit side-chains REVERT: A 138 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6751 (p) REVERT: A 310 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7231 (tpp80) outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.9073 time to fit residues: 58.3171 Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4084 r_free = 0.4084 target = 0.191397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143490 restraints weight = 1495.031| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.21 r_work: 0.3399 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3184 Z= 0.217 Angle : 0.514 5.735 4321 Z= 0.270 Chirality : 0.039 0.135 549 Planarity : 0.003 0.024 527 Dihedral : 3.787 27.333 433 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.07 % Allowed : 20.93 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.40), residues: 406 helix: 1.77 (0.28), residues: 325 sheet: -1.22 (1.11), residues: 18 loop : -0.14 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.001 PHE A 240 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.368 Fit side-chains REVERT: A 138 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6866 (p) REVERT: A 290 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7749 (mm) REVERT: A 310 ARG cc_start: 0.7754 (mmt90) cc_final: 0.7211 (tpp80) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.8530 time to fit residues: 55.0821 Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4076 r_free = 0.4076 target = 0.191239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143323 restraints weight = 1578.128| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.25 r_work: 0.3428 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3184 Z= 0.177 Angle : 0.513 5.231 4321 Z= 0.268 Chirality : 0.039 0.134 549 Planarity : 0.003 0.023 527 Dihedral : 3.751 26.062 433 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 22.67 % Favored : 74.71 % 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 (0.41), residues: 406 helix: 1.82 (0.28), residues: 323 sheet: -0.92 (1.13), residues: 18 loop : -0.34 (0.67), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.010 0.001 TYR A 285 ARG 0.004 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.315 Fit side-chains REVERT: A 138 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6891 (p) REVERT: A 290 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7783 (mm) REVERT: A 310 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7213 (tpp80) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.8621 time to fit residues: 54.8347 Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4100 r_free = 0.4100 target = 0.193246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145485 restraints weight = 1595.352| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.25 r_work: 0.3415 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3184 Z= 0.178 Angle : 0.511 6.441 4321 Z= 0.265 Chirality : 0.039 0.135 549 Planarity : 0.003 0.023 527 Dihedral : 3.696 26.068 433 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.33 % Allowed : 23.55 % Favored : 74.13 % 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 (0.41), residues: 406 helix: 1.92 (0.28), residues: 322 sheet: -0.87 (1.13), residues: 18 loop : -0.28 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.349 Fit side-chains REVERT: A 138 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6916 (p) REVERT: A 290 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7755 (mm) REVERT: A 310 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7242 (tpp80) REVERT: A 439 VAL cc_start: 0.7699 (m) cc_final: 0.7482 (p) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.9140 time to fit residues: 58.8955 Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4120 r_free = 0.4120 target = 0.194829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147510 restraints weight = 1604.888| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.26 r_work: 0.3422 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3184 Z= 0.183 Angle : 0.536 6.787 4321 Z= 0.277 Chirality : 0.039 0.136 549 Planarity : 0.003 0.023 527 Dihedral : 3.732 26.324 433 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 24.71 % Favored : 73.55 % 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: 2.15 (0.41), residues: 406 helix: 1.92 (0.28), residues: 322 sheet: -0.82 (1.12), residues: 18 loop : -0.30 (0.67), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.333 Fit side-chains REVERT: A 138 THR cc_start: 0.7249 (OUTLIER) cc_final: 0.6918 (p) REVERT: A 290 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 310 ARG cc_start: 0.7754 (mmt90) cc_final: 0.7254 (tpp80) REVERT: A 439 VAL cc_start: 0.7629 (m) cc_final: 0.7419 (p) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.8746 time to fit residues: 56.3461 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4128 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.196513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149036 restraints weight = 1664.226| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.29 r_work: 0.3452 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3184 Z= 0.169 Angle : 0.551 10.312 4321 Z= 0.280 Chirality : 0.039 0.149 549 Planarity : 0.003 0.023 527 Dihedral : 3.688 25.580 433 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.03 % Allowed : 24.13 % Favored : 73.84 % 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: 2.12 (0.41), residues: 406 helix: 1.92 (0.29), residues: 322 sheet: -0.86 (1.12), residues: 18 loop : -0.40 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.009 0.001 TYR A 97 ARG 0.003 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.94 seconds wall clock time: 49 minutes 48.01 seconds (2988.01 seconds total)