Starting phenix.real_space_refine on Fri Dec 27 11:43:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.map" model { file = "/net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/12_2024/7yim_33861.cif" } resolution = 2.6 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= 0.095 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 40 5.16 5 C 2925 2.51 5 N 791 2.21 5 O 901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4657 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 570} Time building chain proxies: 3.24, per 1000 atoms: 0.70 Number of scatterers: 4657 At special positions: 0 Unit cell: (69.5594, 91.3616, 103.82, 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 40 16.00 O 901 8.00 N 791 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.00 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.01 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.01 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.01 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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: 1.09 Conformation dependent library (CDL) restraints added in 623.9 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 4.209A pdb=" N ASP A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.750A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.573A pdb=" N GLU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.613A pdb=" N SER A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.629A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 174 through 193 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 231 removed outlier: 3.915A pdb=" N THR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.018A pdb=" N LEU A 305 " --> pdb=" O CYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 361 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.746A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.181A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 7.982A pdb=" N GLU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.204A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.527A pdb=" N GLY A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.999A pdb=" N LYS A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 582 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.913A pdb=" N CYS A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 924 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: 1.33 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1072 1.33 - 1.46: 1193 1.46 - 1.58: 2428 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 4741 Sorted by residual: bond pdb=" CB VAL A 355 " pdb=" CG2 VAL A 355 " ideal model delta sigma weight residual 1.521 1.408 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" C TYR A 174 " pdb=" N ALA A 175 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.09e-02 8.42e+03 1.04e+01 bond pdb=" CG GLN A 245 " pdb=" CD GLN A 245 " ideal model delta sigma weight residual 1.516 1.439 0.077 2.50e-02 1.60e+03 9.56e+00 bond pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.55e+00 bond pdb=" CG1 ILE A 314 " pdb=" CD1 ILE A 314 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.40e+00 ... (remaining 4736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 6228 2.87 - 5.74: 147 5.74 - 8.61: 23 8.61 - 11.48: 1 11.48 - 14.36: 1 Bond angle restraints: 6400 Sorted by residual: angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 128.76 -14.36 2.30e+00 1.89e-01 3.90e+01 angle pdb=" C CYS A 591 " pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sigma weight residual 110.88 103.82 7.06 1.57e+00 4.06e-01 2.02e+01 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.88e+01 angle pdb=" C GLU A 398 " pdb=" N GLU A 399 " pdb=" CA GLU A 399 " ideal model delta sigma weight residual 122.60 116.29 6.31 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C LYS A 581 " pdb=" N CYS A 582 " pdb=" CA CYS A 582 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.82e+00 3.02e-01 1.44e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2536 17.11 - 34.21: 342 34.21 - 51.31: 60 51.31 - 68.42: 19 68.42 - 85.52: 5 Dihedral angle restraints: 2962 sinusoidal: 1222 harmonic: 1740 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 173.66 -80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta harmonic sigma weight residual -180.00 -144.61 -35.39 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 519 0.070 - 0.139: 176 0.139 - 0.209: 19 0.209 - 0.278: 4 0.278 - 0.348: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CB ILE A 481 " pdb=" CA ILE A 481 " pdb=" CG1 ILE A 481 " pdb=" CG2 ILE A 481 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO A 510 " pdb=" N PRO A 510 " pdb=" C PRO A 510 " pdb=" CB PRO A 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 716 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO A 510 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 592 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE A 592 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 592 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 593 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.045 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 176 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.038 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1194 2.80 - 3.32: 4406 3.32 - 3.85: 7985 3.85 - 4.37: 9276 4.37 - 4.90: 15248 Nonbonded interactions: 38109 Sorted by model distance: nonbonded pdb=" OE1 GLU A 165 " pdb=" NH1 ARG A 169 " model vdw 2.272 3.120 nonbonded pdb=" O ARG A 509 " pdb=" OG SER A 513 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 108 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 42 " pdb=" OD2 ASP A 45 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG1 THR A 48 " model vdw 2.311 3.040 ... (remaining 38104 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: 0.290 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 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 : 0.013 0.113 4741 Z= 0.829 Angle : 1.136 14.355 6400 Z= 0.635 Chirality : 0.068 0.348 719 Planarity : 0.009 0.089 837 Dihedral : 15.893 85.522 1782 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.18 % 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: -4.17 (0.25), residues: 590 helix: -2.57 (0.18), residues: 420 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.007 TRP A 181 HIS 0.012 0.003 HIS A 483 PHE 0.031 0.005 PHE A 235 TYR 0.043 0.005 TYR A 185 ARG 0.008 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 1.5949 time to fit residues: 111.9691 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 220 ASN A 389 ASN A 420 GLN A 534 HIS A 555 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4741 Z= 0.211 Angle : 0.577 7.347 6400 Z= 0.312 Chirality : 0.040 0.154 719 Planarity : 0.005 0.051 837 Dihedral : 5.332 30.320 631 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.61 (0.31), residues: 590 helix: -0.47 (0.23), residues: 429 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 181 HIS 0.008 0.001 HIS A 534 PHE 0.016 0.002 PHE A 235 TYR 0.019 0.001 TYR A 185 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6680 (tp) cc_final: 0.6370 (tp) outliers start: 6 outliers final: 1 residues processed: 63 average time/residue: 1.3962 time to fit residues: 91.8573 Evaluate side-chains 46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4741 Z= 0.198 Angle : 0.561 8.757 6400 Z= 0.294 Chirality : 0.040 0.145 719 Planarity : 0.004 0.038 837 Dihedral : 4.764 26.767 631 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.52 % Allowed : 14.73 % Favored : 82.75 % 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: -0.47 (0.33), residues: 590 helix: 0.40 (0.24), residues: 432 sheet: None (None), residues: 0 loop : -2.20 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.006 0.001 HIS A 483 PHE 0.025 0.002 PHE A 50 TYR 0.018 0.001 TYR A 164 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6572 (tp) cc_final: 0.6277 (tp) outliers start: 13 outliers final: 3 residues processed: 56 average time/residue: 1.1674 time to fit residues: 68.4270 Evaluate side-chains 36 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4741 Z= 0.321 Angle : 0.619 7.202 6400 Z= 0.332 Chirality : 0.044 0.142 719 Planarity : 0.005 0.044 837 Dihedral : 4.866 24.367 631 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.71 % Allowed : 17.25 % Favored : 80.04 % 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: -0.62 (0.32), residues: 590 helix: 0.30 (0.23), residues: 426 sheet: None (None), residues: 0 loop : -2.20 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.007 0.002 HIS A 483 PHE 0.037 0.002 PHE A 50 TYR 0.016 0.002 TYR A 185 ARG 0.006 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6737 (tp) cc_final: 0.6395 (tp) REVERT: A 97 GLU cc_start: 0.6257 (tp30) cc_final: 0.5833 (tp30) REVERT: A 448 MET cc_start: 0.6436 (mtp) cc_final: 0.6003 (mtt) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 1.0392 time to fit residues: 59.2259 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4741 Z= 0.227 Angle : 0.577 9.571 6400 Z= 0.305 Chirality : 0.041 0.143 719 Planarity : 0.004 0.039 837 Dihedral : 4.707 22.750 631 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.13 % Allowed : 18.22 % 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: -0.04 (0.33), residues: 590 helix: 0.73 (0.24), residues: 425 sheet: None (None), residues: 0 loop : -1.95 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.007 0.001 HIS A 483 PHE 0.025 0.002 PHE A 50 TYR 0.012 0.001 TYR A 185 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6718 (tp) cc_final: 0.6392 (tp) REVERT: A 97 GLU cc_start: 0.6006 (tp30) cc_final: 0.5645 (tp30) REVERT: A 291 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.5379 (mt0) REVERT: A 403 LYS cc_start: 0.6876 (pttt) cc_final: 0.6488 (tptp) REVERT: A 448 MET cc_start: 0.6329 (mtp) cc_final: 0.5864 (mtt) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.1234 time to fit residues: 62.5159 Evaluate side-chains 43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 4741 Z= 0.443 Angle : 0.715 7.727 6400 Z= 0.383 Chirality : 0.048 0.164 719 Planarity : 0.005 0.048 837 Dihedral : 5.169 24.334 631 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.71 % Allowed : 20.35 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.32), residues: 590 helix: 0.07 (0.24), residues: 423 sheet: None (None), residues: 0 loop : -1.91 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP A 181 HIS 0.010 0.002 HIS A 534 PHE 0.018 0.003 PHE A 235 TYR 0.022 0.002 TYR A 185 ARG 0.004 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 448 MET cc_start: 0.6510 (mtp) cc_final: 0.6042 (mtt) REVERT: A 490 MET cc_start: 0.6107 (mpt) cc_final: 0.5343 (mpt) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.9018 time to fit residues: 51.0018 Evaluate side-chains 44 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 11 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.202 Angle : 0.602 11.210 6400 Z= 0.316 Chirality : 0.042 0.211 719 Planarity : 0.004 0.037 837 Dihedral : 4.587 23.346 631 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.74 % Allowed : 22.48 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.34), residues: 590 helix: 0.89 (0.24), residues: 423 sheet: None (None), residues: 0 loop : -1.68 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 PHE 0.035 0.002 PHE A 50 TYR 0.017 0.001 TYR A 164 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6729 (tp) cc_final: 0.6391 (tp) REVERT: A 403 LYS cc_start: 0.6748 (pttt) cc_final: 0.6357 (tptp) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.0695 time to fit residues: 60.7849 Evaluate side-chains 41 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4741 Z= 0.190 Angle : 0.584 9.994 6400 Z= 0.308 Chirality : 0.040 0.185 719 Planarity : 0.004 0.034 837 Dihedral : 4.379 22.403 631 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.36 % Allowed : 23.45 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.35), residues: 590 helix: 1.13 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -1.50 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 181 HIS 0.005 0.001 HIS A 483 PHE 0.033 0.002 PHE A 54 TYR 0.009 0.001 TYR A 505 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.561 Fit side-chains REVERT: A 43 LEU cc_start: 0.6661 (tp) cc_final: 0.6301 (tp) REVERT: A 403 LYS cc_start: 0.6595 (pttt) cc_final: 0.6368 (tptp) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 1.1581 time to fit residues: 57.4048 Evaluate side-chains 37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 583 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 34 optimal weight: 0.0070 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4741 Z= 0.187 Angle : 0.583 10.429 6400 Z= 0.307 Chirality : 0.040 0.135 719 Planarity : 0.004 0.034 837 Dihedral : 4.229 23.828 631 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 24.03 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.35), residues: 590 helix: 1.34 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -1.40 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 181 HIS 0.006 0.001 HIS A 534 PHE 0.031 0.002 PHE A 50 TYR 0.016 0.001 TYR A 164 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.622 Fit side-chains REVERT: A 43 LEU cc_start: 0.6691 (tp) cc_final: 0.6335 (tp) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 1.0770 time to fit residues: 53.4072 Evaluate side-chains 34 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4741 Z= 0.201 Angle : 0.619 10.827 6400 Z= 0.324 Chirality : 0.041 0.146 719 Planarity : 0.004 0.035 837 Dihedral : 4.240 23.005 631 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.16 % Allowed : 24.61 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.35), residues: 590 helix: 1.31 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -1.33 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 PHE 0.027 0.002 PHE A 50 TYR 0.008 0.001 TYR A 404 ARG 0.003 0.000 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.530 Fit side-chains REVERT: A 43 LEU cc_start: 0.6704 (tp) cc_final: 0.6343 (tp) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 1.0668 time to fit residues: 45.1453 Evaluate side-chains 35 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.206360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.160514 restraints weight = 5347.096| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.45 r_work: 0.4239 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4741 Z= 0.230 Angle : 0.634 10.985 6400 Z= 0.332 Chirality : 0.042 0.174 719 Planarity : 0.004 0.037 837 Dihedral : 4.302 22.761 631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.97 % Allowed : 24.22 % Favored : 74.81 % 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: 0.75 (0.35), residues: 590 helix: 1.16 (0.24), residues: 435 sheet: None (None), residues: 0 loop : -1.31 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.007 0.001 HIS A 534 PHE 0.035 0.002 PHE A 252 TYR 0.017 0.002 TYR A 164 ARG 0.003 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.82 seconds wall clock time: 34 minutes 18.04 seconds (2058.04 seconds total)