Starting phenix.real_space_refine on Thu Nov 14 02:37:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/11_2024/8sc1_40334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/11_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_40334/11_2024/8sc1_40334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/11_2024/8sc1_40334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/11_2024/8sc1_40334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc1_40334/11_2024/8sc1_40334.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.59, per 1000 atoms: 0.75 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 - 3.00 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: 1.11 Conformation dependent library (CDL) restraints added in 564.9 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: 0.43 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: 0.96 Time building geometry restraints manager: 1.25 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: 0.00 - 1.21: 4509 1.21 - 2.42: 252 2.42 - 3.64: 40 3.64 - 4.85: 12 4.85 - 6.06: 8 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 3.040 nonbonded pdb=" NH2 ARG A 402 " pdb=" OE2 GLU A 455 " model vdw 2.384 3.120 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.476 3.040 nonbonded pdb=" N ASP A 426 " pdb=" OD1 ASP A 426 " model vdw 2.508 3.120 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.564 3.120 ... (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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.421 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: 1.0114 time to fit residues: 55.7818 Evaluate side-chains 36 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3537 Z= 0.215 Angle : 0.612 6.605 4821 Z= 0.316 Chirality : 0.038 0.118 561 Planarity : 0.005 0.035 597 Dihedral : 4.139 15.543 480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.43 % Allowed : 4.05 % Favored : 93.51 % 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: 1.04 (0.40), residues: 442 helix: 0.75 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.91 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 261 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.002 PHE A 32 TYR 0.010 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 43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.328 Fit side-chains REVERT: A 51 GLN cc_start: 0.8406 (tt0) cc_final: 0.7866 (tm-30) REVERT: A 92 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: A 218 MET cc_start: 0.7445 (mmm) cc_final: 0.7197 (mmm) REVERT: A 396 THR cc_start: 0.7877 (m) cc_final: 0.7549 (p) REVERT: A 408 MET cc_start: 0.8051 (mmm) cc_final: 0.7826 (mmm) REVERT: A 492 GLN cc_start: 0.6801 (mt0) cc_final: 0.6294 (tp-100) outliers start: 9 outliers final: 1 residues processed: 40 average time/residue: 0.9882 time to fit residues: 41.2321 Evaluate side-chains 32 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 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: 0.7810 moved from start: 0.1985 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= 0.199 Angle : 0.566 6.115 4821 Z= 0.292 Chirality : 0.037 0.116 561 Planarity : 0.005 0.034 597 Dihedral : 3.873 14.945 480 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.43 % Allowed : 5.95 % Favored : 91.62 % 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: 1.58 (0.40), residues: 442 helix: 1.16 (0.29), residues: 314 sheet: None (None), residues: 0 loop : 1.10 (0.60), residues: 128 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 0.007 0.001 TYR A 457 ARG 0.003 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 47 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.395 Fit side-chains REVERT: A 51 GLN cc_start: 0.8383 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 92 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: A 396 THR cc_start: 0.7757 (m) cc_final: 0.7330 (p) REVERT: A 408 MET cc_start: 0.8075 (mmm) cc_final: 0.7846 (mmm) REVERT: A 451 LEU cc_start: 0.6956 (mp) cc_final: 0.6514 (tt) REVERT: A 492 GLN cc_start: 0.6975 (mt0) cc_final: 0.6722 (tm-30) outliers start: 9 outliers final: 3 residues processed: 44 average time/residue: 1.0125 time to fit residues: 46.4711 Evaluate side-chains 41 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.2324 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 : 0.565 6.109 4821 Z= 0.291 Chirality : 0.037 0.117 561 Planarity : 0.005 0.036 597 Dihedral : 3.789 14.415 480 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 1.63 (0.40), residues: 442 helix: 1.28 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.86 (0.57), 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 0.012 0.001 PHE A 22 TYR 0.007 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 to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.371 Fit side-chains REVERT: A 51 GLN cc_start: 0.8426 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 92 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: A 239 MET cc_start: 0.6263 (ptp) cc_final: 0.5414 (tpt) REVERT: A 396 THR cc_start: 0.7738 (m) cc_final: 0.7296 (p) REVERT: A 408 MET cc_start: 0.8087 (mmm) cc_final: 0.7861 (mmm) REVERT: A 451 LEU cc_start: 0.7049 (mp) cc_final: 0.6536 (tt) outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.9136 time to fit residues: 45.8484 Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2521 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= 0.217 Angle : 0.572 6.245 4821 Z= 0.295 Chirality : 0.038 0.120 561 Planarity : 0.005 0.040 597 Dihedral : 3.763 13.321 480 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.97 % Allowed : 8.11 % Favored : 88.92 % 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: 1.66 (0.40), residues: 442 helix: 1.31 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.86 (0.57), 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 0.012 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 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 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.336 Fit side-chains REVERT: A 51 GLN cc_start: 0.8434 (tt0) cc_final: 0.7885 (tm-30) REVERT: A 92 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 396 THR cc_start: 0.7788 (m) cc_final: 0.7303 (p) REVERT: A 408 MET cc_start: 0.8100 (mmm) cc_final: 0.7840 (mmm) REVERT: A 451 LEU cc_start: 0.7139 (mp) cc_final: 0.6623 (tt) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.9094 time to fit residues: 40.9355 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3537 Z= 0.154 Angle : 0.513 5.597 4821 Z= 0.265 Chirality : 0.036 0.114 561 Planarity : 0.004 0.036 597 Dihedral : 3.631 17.500 480 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 9.19 % 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: 2.13 (0.41), residues: 442 helix: 1.65 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.05 (0.57), residues: 128 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 0.013 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 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 to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.369 Fit side-chains REVERT: A 51 GLN cc_start: 0.8369 (tt0) cc_final: 0.7838 (tm-30) REVERT: A 92 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 239 MET cc_start: 0.6232 (ptp) cc_final: 0.5348 (tpt) REVERT: A 396 THR cc_start: 0.7774 (m) cc_final: 0.7307 (p) REVERT: A 408 MET cc_start: 0.8080 (mmm) cc_final: 0.7820 (mmm) REVERT: A 451 LEU cc_start: 0.7199 (mp) cc_final: 0.6678 (tt) outliers start: 8 outliers final: 3 residues processed: 44 average time/residue: 0.9270 time to fit residues: 42.6388 Evaluate side-chains 39 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3537 Z= 0.159 Angle : 0.511 5.567 4821 Z= 0.263 Chirality : 0.036 0.119 561 Planarity : 0.004 0.037 597 Dihedral : 3.582 17.415 480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.70 % Allowed : 8.92 % 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: 2.16 (0.41), residues: 442 helix: 1.70 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 0.98 (0.58), residues: 126 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 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 47 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.379 Fit side-chains REVERT: A 51 GLN cc_start: 0.8364 (tt0) cc_final: 0.7819 (tm-30) REVERT: A 92 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: A 396 THR cc_start: 0.7782 (m) cc_final: 0.7321 (p) REVERT: A 408 MET cc_start: 0.8065 (mmm) cc_final: 0.7803 (mmm) REVERT: A 451 LEU cc_start: 0.7161 (mp) cc_final: 0.6653 (tt) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 0.9955 time to fit residues: 44.6504 Evaluate side-chains 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 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 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: 0.9990 chunk 3 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7772 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3537 Z= 0.150 Angle : 0.508 5.482 4821 Z= 0.262 Chirality : 0.035 0.116 561 Planarity : 0.004 0.035 597 Dihedral : 3.530 17.504 480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 10.00 % 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: 2.56 (0.41), residues: 442 helix: 1.96 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.31 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.009 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 49 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.395 Fit side-chains REVERT: A 51 GLN cc_start: 0.8349 (tt0) cc_final: 0.7807 (tm-30) REVERT: A 92 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: A 239 MET cc_start: 0.6173 (ptp) cc_final: 0.5047 (tpt) REVERT: A 396 THR cc_start: 0.7792 (m) cc_final: 0.7322 (p) REVERT: A 408 MET cc_start: 0.8064 (mmm) cc_final: 0.7801 (mmm) REVERT: A 451 LEU cc_start: 0.7132 (mp) cc_final: 0.6650 (tt) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.9231 time to fit residues: 44.3679 Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 505 LEU 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: 0.6980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3537 Z= 0.153 Angle : 0.507 5.493 4821 Z= 0.260 Chirality : 0.035 0.115 561 Planarity : 0.004 0.036 597 Dihedral : 3.505 17.022 480 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 9.73 % 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: 2.46 (0.41), residues: 442 helix: 1.88 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.25 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.009 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 to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.322 Fit side-chains REVERT: A 51 GLN cc_start: 0.8372 (tt0) cc_final: 0.7811 (tm-30) REVERT: A 92 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 239 MET cc_start: 0.6233 (ptp) cc_final: 0.5058 (tpt) REVERT: A 396 THR cc_start: 0.7780 (m) cc_final: 0.7319 (p) REVERT: A 408 MET cc_start: 0.8070 (mmm) cc_final: 0.7810 (mmm) REVERT: A 451 LEU cc_start: 0.7176 (mp) cc_final: 0.6685 (tt) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.9807 time to fit residues: 43.8797 Evaluate side-chains 46 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.7772 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3537 Z= 0.151 Angle : 0.502 5.479 4821 Z= 0.258 Chirality : 0.035 0.116 561 Planarity : 0.004 0.036 597 Dihedral : 3.486 17.180 480 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 2.55 (0.41), residues: 442 helix: 1.92 (0.30), residues: 310 sheet: None (None), residues: 0 loop : 1.37 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.009 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 46 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.360 Fit side-chains REVERT: A 51 GLN cc_start: 0.8352 (tt0) cc_final: 0.7782 (tm-30) REVERT: A 92 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: A 239 MET cc_start: 0.6250 (ptp) cc_final: 0.5079 (tpt) REVERT: A 396 THR cc_start: 0.7776 (m) cc_final: 0.7308 (p) REVERT: A 408 MET cc_start: 0.8068 (mmm) cc_final: 0.7810 (mmm) REVERT: A 451 LEU cc_start: 0.7145 (mp) cc_final: 0.6667 (tt) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.9439 time to fit residues: 42.3415 Evaluate side-chains 43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.200312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155337 restraints weight = 3592.844| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.96 r_work: 0.3493 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3537 Z= 0.145 Angle : 0.493 5.452 4821 Z= 0.253 Chirality : 0.035 0.116 561 Planarity : 0.004 0.035 597 Dihedral : 3.449 16.963 480 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 2.63 (0.41), residues: 442 helix: 1.97 (0.30), residues: 310 sheet: None (None), residues: 0 loop : 1.42 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.009 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: 1518.53 seconds wall clock time: 28 minutes 4.28 seconds (1684.28 seconds total)