Starting phenix.real_space_refine on Sun Mar 10 17:12:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/03_2024/8sc1_40334.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 30 5.16 5 C 2270 2.51 5 N 559 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3447 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3447 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.71 Number of scatterers: 3447 At special positions: 0 Unit cell: (92.02, 84.28, 65.36, 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 30 16.00 O 588 8.00 N 559 7.00 C 2270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.36 Conformation dependent library (CDL) restraints added in 664.4 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 83.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.559A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.873A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.997A pdb=" N SER A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 146 through 173 removed outlier: 3.961A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.953A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.838A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.705A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 271 - end of helix removed outlier: 3.881A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.522A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 removed outlier: 3.551A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.558A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.682A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.537A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 4.048A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 4.522A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 removed outlier: 3.626A pdb=" N ILE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.742A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.540A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 238 hydrogen bonds defined for protein. 684 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: 0.95 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1064 1.35 - 1.47: 908 1.47 - 1.59: 1520 1.59 - 1.71: 0 1.71 - 1.84: 45 Bond restraints: 3537 Sorted by residual: bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.29e-02 6.01e+03 7.91e-01 bond pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " ideal model delta sigma weight residual 1.808 1.836 -0.028 3.30e-02 9.18e+02 6.96e-01 bond pdb=" CA LEU A 494 " pdb=" C LEU A 494 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.91e-01 bond pdb=" C ILE A 387 " pdb=" O ILE A 387 " ideal model delta sigma weight residual 1.240 1.250 -0.010 1.26e-02 6.30e+03 6.41e-01 bond pdb=" C GLY A 253 " pdb=" O GLY A 253 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.35e-02 5.49e+03 5.59e-01 ... (remaining 3532 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 120 106.98 - 113.72: 1906 113.72 - 120.47: 1497 120.47 - 127.22: 1251 127.22 - 133.96: 47 Bond angle restraints: 4821 Sorted by residual: angle pdb=" N VAL A 212 " pdb=" CA VAL A 212 " pdb=" C VAL A 212 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" CA CYS A 121 " pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " ideal model delta sigma weight residual 114.40 120.46 -6.06 2.30e+00 1.89e-01 6.94e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.45 -6.05 2.30e+00 1.89e-01 6.93e+00 angle pdb=" N TYR A 404 " pdb=" CA TYR A 404 " pdb=" C TYR A 404 " ideal model delta sigma weight residual 109.81 115.25 -5.44 2.21e+00 2.05e-01 6.05e+00 angle pdb=" CA TRP A 261 " pdb=" CB TRP A 261 " pdb=" CG TRP A 261 " ideal model delta sigma weight residual 113.60 118.11 -4.51 1.90e+00 2.77e-01 5.64e+00 ... (remaining 4816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 1924 14.66 - 29.32: 99 29.32 - 43.97: 24 43.97 - 58.63: 9 58.63 - 73.29: 2 Dihedral angle restraints: 2058 sinusoidal: 782 harmonic: 1276 Sorted by residual: dihedral pdb=" CA TYR A 72 " pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA CYS A 50 " pdb=" C CYS A 50 " pdb=" N GLN A 51 " pdb=" CA GLN A 51 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG A 399 " pdb=" C ARG A 399 " pdb=" N VAL A 400 " pdb=" CA VAL A 400 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 321 0.027 - 0.055: 158 0.055 - 0.082: 54 0.082 - 0.110: 14 0.110 - 0.137: 14 Chirality restraints: 561 Sorted by residual: chirality pdb=" CA PRO A 341 " pdb=" N PRO A 341 " pdb=" C PRO A 341 " pdb=" CB PRO A 341 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA TYR A 72 " pdb=" N TYR A 72 " pdb=" C TYR A 72 " pdb=" CB TYR A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 558 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C THR A 182 " -0.049 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 72 " 0.011 2.00e-02 2.50e+03 1.70e-02 5.78e+00 pdb=" CG TYR A 72 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 72 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 72 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 72 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 72 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 72 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 206 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ARG A 206 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 206 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 207 " 0.013 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 781 2.79 - 3.32: 3376 3.32 - 3.85: 5235 3.85 - 4.37: 6164 4.37 - 4.90: 10862 Nonbonded interactions: 26418 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.266 2.440 nonbonded pdb=" NH2 ARG A 402 " pdb=" OE2 GLU A 455 " model vdw 2.384 2.520 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.476 2.440 nonbonded pdb=" N ASP A 426 " pdb=" OD1 ASP A 426 " model vdw 2.508 2.520 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.564 2.520 ... (remaining 26413 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: 0.790 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: 3.640 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 0.028 3537 Z= 0.178 Angle : 0.679 6.060 4821 Z= 0.396 Chirality : 0.040 0.137 561 Planarity : 0.008 0.058 597 Dihedral : 10.470 73.290 1233 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 (0.39), residues: 442 helix: -1.04 (0.27), residues: 298 sheet: None (None), residues: 0 loop : 1.20 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 261 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.002 PHE A 22 TYR 0.023 0.003 TYR A 72 ARG 0.015 0.002 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.355 Fit side-chains REVERT: A 51 GLN cc_start: 0.8286 (tt0) cc_final: 0.7836 (mm-40) REVERT: A 218 MET cc_start: 0.7361 (mmm) cc_final: 0.6832 (mtm) REVERT: A 351 MET cc_start: 0.8254 (mtt) cc_final: 0.7981 (mtm) REVERT: A 396 THR cc_start: 0.7819 (m) cc_final: 0.7451 (p) REVERT: A 408 MET cc_start: 0.8154 (mmm) cc_final: 0.7936 (mmm) REVERT: A 480 THR cc_start: 0.7728 (m) cc_final: 0.7442 (m) REVERT: A 492 GLN cc_start: 0.6991 (mt0) cc_final: 0.6666 (tp-100) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.9689 time to fit residues: 53.4031 Evaluate side-chains 36 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3537 Z= 0.167 Angle : 0.562 6.294 4821 Z= 0.291 Chirality : 0.037 0.115 561 Planarity : 0.004 0.034 597 Dihedral : 4.033 15.657 480 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.70 % Allowed : 4.59 % Favored : 92.70 % 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: 1.32 (0.40), residues: 442 helix: 0.93 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 1.12 (0.60), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 32 TYR 0.008 0.001 TYR A 240 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.420 Fit side-chains REVERT: A 51 GLN cc_start: 0.8320 (tt0) cc_final: 0.7822 (tm-30) REVERT: A 92 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: A 239 MET cc_start: 0.6292 (ptp) cc_final: 0.5385 (tpt) REVERT: A 396 THR cc_start: 0.7893 (m) cc_final: 0.7558 (p) REVERT: A 408 MET cc_start: 0.8029 (mmm) cc_final: 0.7810 (mmm) REVERT: A 492 GLN cc_start: 0.6716 (mt0) cc_final: 0.6157 (tp-100) outliers start: 10 outliers final: 1 residues processed: 43 average time/residue: 0.9561 time to fit residues: 42.9588 Evaluate side-chains 33 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3537 Z= 0.205 Angle : 0.577 6.417 4821 Z= 0.298 Chirality : 0.038 0.118 561 Planarity : 0.005 0.033 597 Dihedral : 3.889 14.893 480 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.89 % Allowed : 6.22 % Favored : 91.89 % 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: 1.57 (0.40), residues: 442 helix: 1.19 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.99 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 151 TYR 0.008 0.001 TYR A 457 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.390 Fit side-chains REVERT: A 51 GLN cc_start: 0.8409 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 92 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 396 THR cc_start: 0.7738 (m) cc_final: 0.7314 (p) REVERT: A 408 MET cc_start: 0.8070 (mmm) cc_final: 0.7848 (mmm) REVERT: A 451 LEU cc_start: 0.6965 (mp) cc_final: 0.6507 (tt) REVERT: A 492 GLN cc_start: 0.6981 (mt0) cc_final: 0.6757 (tm-30) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.8681 time to fit residues: 38.2243 Evaluate side-chains 41 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.0070 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3537 Z= 0.147 Angle : 0.502 5.525 4821 Z= 0.258 Chirality : 0.035 0.113 561 Planarity : 0.004 0.031 597 Dihedral : 3.663 14.643 480 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.97 % Allowed : 6.49 % Favored : 90.54 % 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: 442 helix: 1.63 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 1.12 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.006 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.372 Fit side-chains REVERT: A 51 GLN cc_start: 0.8302 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 92 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: A 180 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7083 (tp) REVERT: A 239 MET cc_start: 0.6212 (ptp) cc_final: 0.5250 (tpt) REVERT: A 396 THR cc_start: 0.7735 (m) cc_final: 0.7324 (p) REVERT: A 408 MET cc_start: 0.8054 (mmm) cc_final: 0.7831 (mmm) REVERT: A 451 LEU cc_start: 0.6957 (mp) cc_final: 0.6465 (tt) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 0.8713 time to fit residues: 43.7193 Evaluate side-chains 41 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3537 Z= 0.206 Angle : 0.558 6.348 4821 Z= 0.286 Chirality : 0.037 0.118 561 Planarity : 0.005 0.038 597 Dihedral : 3.719 13.432 480 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.24 % Allowed : 7.03 % Favored : 89.73 % 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 (0.41), residues: 442 helix: 1.45 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 0.89 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.367 Fit side-chains REVERT: A 51 GLN cc_start: 0.8361 (tt0) cc_final: 0.7818 (tm-30) REVERT: A 92 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: A 396 THR cc_start: 0.7790 (m) cc_final: 0.7384 (p) REVERT: A 408 MET cc_start: 0.8098 (mmm) cc_final: 0.7844 (mmt) REVERT: A 451 LEU cc_start: 0.7096 (mp) cc_final: 0.6592 (tt) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.9992 time to fit residues: 45.7915 Evaluate side-chains 45 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3537 Z= 0.204 Angle : 0.558 6.132 4821 Z= 0.288 Chirality : 0.037 0.117 561 Planarity : 0.005 0.039 597 Dihedral : 3.754 17.171 480 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 7.84 % Favored : 89.46 % 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: 1.88 (0.41), residues: 442 helix: 1.48 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 0.88 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.351 Fit side-chains REVERT: A 51 GLN cc_start: 0.8355 (tt0) cc_final: 0.7800 (tm-30) REVERT: A 92 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: A 239 MET cc_start: 0.6287 (ptp) cc_final: 0.5461 (tpt) REVERT: A 396 THR cc_start: 0.7836 (m) cc_final: 0.7414 (p) REVERT: A 408 MET cc_start: 0.8092 (mmm) cc_final: 0.7839 (mmm) REVERT: A 451 LEU cc_start: 0.7205 (mp) cc_final: 0.6670 (tt) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.9412 time to fit residues: 42.2015 Evaluate side-chains 45 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3537 Z= 0.196 Angle : 0.545 6.048 4821 Z= 0.281 Chirality : 0.037 0.116 561 Planarity : 0.005 0.040 597 Dihedral : 3.734 16.450 480 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.70 % Allowed : 8.65 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.41), residues: 442 helix: 1.43 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.81 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.457 Fit side-chains REVERT: A 51 GLN cc_start: 0.8357 (tt0) cc_final: 0.7779 (tm-30) REVERT: A 92 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 396 THR cc_start: 0.7818 (m) cc_final: 0.7392 (p) REVERT: A 408 MET cc_start: 0.8096 (mmm) cc_final: 0.7844 (mmt) REVERT: A 451 LEU cc_start: 0.7283 (mp) cc_final: 0.6753 (tt) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.9778 time to fit residues: 42.8379 Evaluate side-chains 44 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3537 Z= 0.168 Angle : 0.528 5.649 4821 Z= 0.272 Chirality : 0.036 0.112 561 Planarity : 0.004 0.037 597 Dihedral : 3.644 16.506 480 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.24 % Allowed : 8.65 % Favored : 88.11 % 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: 2.08 (0.41), residues: 442 helix: 1.65 (0.30), residues: 318 sheet: None (None), residues: 0 loop : 0.89 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.344 Fit side-chains REVERT: A 51 GLN cc_start: 0.8323 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 92 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 239 MET cc_start: 0.6238 (ptp) cc_final: 0.5098 (tpt) REVERT: A 396 THR cc_start: 0.7804 (m) cc_final: 0.7396 (p) REVERT: A 408 MET cc_start: 0.8056 (mmm) cc_final: 0.7798 (mmt) REVERT: A 451 LEU cc_start: 0.7219 (mp) cc_final: 0.6723 (tt) outliers start: 12 outliers final: 6 residues processed: 45 average time/residue: 0.8704 time to fit residues: 40.8928 Evaluate side-chains 46 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 41 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3537 Z= 0.134 Angle : 0.485 5.402 4821 Z= 0.249 Chirality : 0.035 0.115 561 Planarity : 0.004 0.034 597 Dihedral : 3.465 16.118 480 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.89 % Allowed : 9.73 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.42), residues: 442 helix: 1.88 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 1.09 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.366 Fit side-chains REVERT: A 51 GLN cc_start: 0.8274 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 92 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: A 239 MET cc_start: 0.6292 (ptp) cc_final: 0.5125 (tpt) REVERT: A 396 THR cc_start: 0.7799 (m) cc_final: 0.7408 (p) REVERT: A 402 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5450 (mtm-85) REVERT: A 408 MET cc_start: 0.8051 (mmm) cc_final: 0.7797 (mmt) REVERT: A 451 LEU cc_start: 0.7115 (mp) cc_final: 0.6643 (tt) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 1.0131 time to fit residues: 45.4526 Evaluate side-chains 41 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3537 Z= 0.178 Angle : 0.533 5.813 4821 Z= 0.274 Chirality : 0.036 0.117 561 Planarity : 0.004 0.038 597 Dihedral : 3.584 15.756 480 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.62 % Allowed : 10.00 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.41), residues: 442 helix: 1.70 (0.30), residues: 318 sheet: None (None), residues: 0 loop : 0.88 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.435 Fit side-chains REVERT: A 51 GLN cc_start: 0.8292 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 92 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: A 239 MET cc_start: 0.6296 (ptp) cc_final: 0.5429 (tpt) REVERT: A 396 THR cc_start: 0.7864 (m) cc_final: 0.7475 (p) REVERT: A 408 MET cc_start: 0.8074 (mmm) cc_final: 0.7821 (mmt) REVERT: A 451 LEU cc_start: 0.7194 (mp) cc_final: 0.6705 (tt) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 1.1774 time to fit residues: 46.5679 Evaluate side-chains 40 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.194863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149329 restraints weight = 3590.860| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.12 r_work: 0.3428 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3537 Z= 0.206 Angle : 0.560 6.088 4821 Z= 0.288 Chirality : 0.037 0.128 561 Planarity : 0.004 0.037 597 Dihedral : 3.689 15.793 480 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.89 % Allowed : 10.27 % Favored : 87.84 % 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: 1.94 (0.40), residues: 442 helix: 1.56 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 0.80 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 428 PHE 0.012 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.12 seconds wall clock time: 28 minutes 28.41 seconds (1708.41 seconds total)