Starting phenix.real_space_refine on Fri Dec 27 08:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc2_40335/12_2024/8sc2_40335.cif" } resolution = 3.36 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= 0.018 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 32 5.16 5 C 2330 2.51 5 N 572 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3534 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3505 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 24, 'TRANS': 428} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'C9F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.95, per 1000 atoms: 0.83 Number of scatterers: 3534 At special positions: 0 Unit cell: (88.2, 82.32, 66.36, 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 32 16.00 O 600 8.00 N 572 7.00 C 2330 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 361.0 milliseconds 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 830 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 82.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 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 73 removed outlier: 3.786A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 105 through 109 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: 4.064A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.848A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.712A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.604A pdb=" N VAL A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 335 through 340 removed outlier: 4.479A pdb=" N THR A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.503A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.025A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 Processing helix chain 'A' and resid 427 through 457 removed outlier: 3.668A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 3.962A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.552A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 240 hydrogen bonds defined for protein. 699 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: 0.93 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 637 1.33 - 1.45: 975 1.45 - 1.58: 1970 1.58 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 3630 Sorted by residual: bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.96e+00 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.19e+00 bond pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N LEU A 251 " pdb=" CA LEU A 251 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 bond pdb=" N TRP A 64 " pdb=" CA TRP A 64 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.24e-02 6.50e+03 5.82e+00 ... (remaining 3625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4713 1.07 - 2.14: 177 2.14 - 3.20: 44 3.20 - 4.27: 12 4.27 - 5.34: 5 Bond angle restraints: 4951 Sorted by residual: angle pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" O ILE A 365 " ideal model delta sigma weight residual 120.95 117.51 3.44 1.04e+00 9.25e-01 1.10e+01 angle pdb=" CA CYS A 36 " pdb=" C CYS A 36 " pdb=" O CYS A 36 " ideal model delta sigma weight residual 120.70 117.45 3.25 1.03e+00 9.43e-01 9.93e+00 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 120.57 117.59 2.98 1.07e+00 8.73e-01 7.78e+00 angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.49e+00 angle pdb=" N ASP A 149 " pdb=" CA ASP A 149 " pdb=" C ASP A 149 " ideal model delta sigma weight residual 111.71 108.79 2.92 1.15e+00 7.56e-01 6.43e+00 ... (remaining 4946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.24: 1889 9.24 - 18.49: 164 18.49 - 27.73: 47 27.73 - 36.98: 17 36.98 - 46.22: 6 Dihedral angle restraints: 2123 sinusoidal: 826 harmonic: 1297 Sorted by residual: dihedral pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" CB LEU A 192 " pdb=" CG LEU A 192 " ideal model delta sinusoidal sigma weight residual -60.00 -101.37 41.37 3 1.50e+01 4.44e-03 7.40e+00 dihedral pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" CB GLN A 241 " pdb=" CG GLN A 241 " ideal model delta sinusoidal sigma weight residual -180.00 -140.11 -39.89 3 1.50e+01 4.44e-03 7.09e+00 dihedral pdb=" C ILE A 365 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" CB ILE A 365 " ideal model delta harmonic sigma weight residual -122.00 -128.63 6.63 0 2.50e+00 1.60e-01 7.04e+00 ... (remaining 2120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 447 0.044 - 0.087: 93 0.087 - 0.130: 26 0.130 - 0.174: 3 0.174 - 0.217: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LEU A 248 " pdb=" N LEU A 248 " pdb=" C LEU A 248 " pdb=" CB LEU A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 35 " pdb=" CA ILE A 35 " pdb=" CG1 ILE A 35 " pdb=" CG2 ILE A 35 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 568 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C VAL A 40 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 40 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 196 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 258 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 259 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.016 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 839 2.79 - 3.31: 3487 3.31 - 3.84: 5626 3.84 - 4.37: 6374 4.37 - 4.90: 11282 Nonbonded interactions: 27608 Sorted by model distance: nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.258 3.040 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 3.040 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.297 3.040 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.317 3.040 nonbonded pdb=" O CYS A 142 " pdb=" OG SER A 145 " model vdw 2.360 3.040 ... (remaining 27603 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: 0.760 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.050 Find NCS groups from input model: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.038 3630 Z= 0.207 Angle : 0.551 5.341 4951 Z= 0.345 Chirality : 0.041 0.217 571 Planarity : 0.004 0.036 612 Dihedral : 8.521 46.221 1284 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: 2.79 (0.42), residues: 449 helix: 2.07 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.57 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.007 0.001 TYR A 168 ARG 0.002 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8480 (tpt) cc_final: 0.8139 (tpt) REVERT: A 431 ASN cc_start: 0.8059 (t0) cc_final: 0.7805 (t0) REVERT: A 435 MET cc_start: 0.8132 (tpp) cc_final: 0.7737 (tpp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1586 time to fit residues: 21.0230 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3630 Z= 0.194 Angle : 0.571 7.853 4951 Z= 0.286 Chirality : 0.040 0.214 571 Planarity : 0.004 0.037 612 Dihedral : 4.259 28.936 516 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.86 % Allowed : 9.02 % Favored : 89.12 % 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: 2.88 (0.42), residues: 449 helix: 2.12 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.66 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 334 TYR 0.013 0.001 TYR A 72 ARG 0.005 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (t0) REVERT: A 431 ASN cc_start: 0.8063 (t0) cc_final: 0.7713 (t0) REVERT: A 435 MET cc_start: 0.8105 (tpp) cc_final: 0.7783 (tpp) REVERT: A 498 LEU cc_start: 0.7978 (tt) cc_final: 0.7532 (mm) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1269 time to fit residues: 14.9081 Evaluate side-chains 85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3630 Z= 0.183 Angle : 0.550 6.503 4951 Z= 0.274 Chirality : 0.040 0.180 571 Planarity : 0.004 0.030 612 Dihedral : 4.364 36.256 516 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 10.88 % Favored : 86.74 % 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: 2.80 (0.42), residues: 449 helix: 2.08 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.57 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.009 0.001 PHE A 32 TYR 0.013 0.001 TYR A 72 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 284 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: A 431 ASN cc_start: 0.8058 (t0) cc_final: 0.7697 (t0) REVERT: A 435 MET cc_start: 0.8113 (tpp) cc_final: 0.7791 (tpp) REVERT: A 479 ILE cc_start: 0.6964 (mm) cc_final: 0.6736 (mt) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1304 time to fit residues: 14.4128 Evaluate side-chains 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3630 Z= 0.220 Angle : 0.558 8.827 4951 Z= 0.277 Chirality : 0.040 0.196 571 Planarity : 0.004 0.034 612 Dihedral : 4.341 32.230 516 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.92 % Allowed : 11.67 % Favored : 85.41 % 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: 2.69 (0.42), residues: 449 helix: 2.01 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.48 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 32 TYR 0.013 0.001 TYR A 72 ARG 0.003 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 284 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6243 (mt-10) REVERT: A 435 MET cc_start: 0.8094 (tpp) cc_final: 0.7772 (tpp) REVERT: A 448 MET cc_start: 0.8395 (mmm) cc_final: 0.8056 (mmm) REVERT: A 479 ILE cc_start: 0.7061 (mm) cc_final: 0.6835 (mt) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.1214 time to fit residues: 13.3092 Evaluate side-chains 81 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.0670 chunk 17 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3630 Z= 0.149 Angle : 0.541 9.208 4951 Z= 0.260 Chirality : 0.038 0.199 571 Planarity : 0.004 0.031 612 Dihedral : 4.302 34.149 516 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.92 % Allowed : 12.47 % Favored : 84.62 % 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: 2.89 (0.42), residues: 449 helix: 2.18 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.52 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.001 0.000 HIS A 49 PHE 0.015 0.001 PHE A 334 TYR 0.006 0.001 TYR A 256 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 284 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6307 (mt-10) REVERT: A 431 ASN cc_start: 0.8042 (t0) cc_final: 0.7703 (t0) REVERT: A 435 MET cc_start: 0.8059 (tpp) cc_final: 0.7739 (tpp) REVERT: A 448 MET cc_start: 0.8322 (mmm) cc_final: 0.8011 (mmm) REVERT: A 472 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 498 LEU cc_start: 0.7988 (tt) cc_final: 0.7466 (mm) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 0.1426 time to fit residues: 16.1788 Evaluate side-chains 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 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: 0.8062 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3630 Z= 0.212 Angle : 0.593 9.186 4951 Z= 0.287 Chirality : 0.042 0.273 571 Planarity : 0.004 0.034 612 Dihedral : 4.274 30.416 516 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.92 % Allowed : 15.38 % Favored : 81.70 % 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: 2.71 (0.42), residues: 449 helix: 2.02 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.50 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.012 0.001 TYR A 72 ARG 0.003 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7387 (ptt180) cc_final: 0.6895 (ptt90) REVERT: A 284 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6306 (mt-10) REVERT: A 435 MET cc_start: 0.8082 (tpp) cc_final: 0.7788 (tpp) REVERT: A 448 MET cc_start: 0.8360 (mmm) cc_final: 0.8030 (mmm) REVERT: A 472 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 498 LEU cc_start: 0.8036 (tt) cc_final: 0.7474 (mm) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.1491 time to fit residues: 15.4173 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.3872 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3630 Z= 0.145 Angle : 0.554 9.158 4951 Z= 0.265 Chirality : 0.040 0.234 571 Planarity : 0.004 0.031 612 Dihedral : 4.188 36.603 516 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.65 % Allowed : 16.45 % Favored : 80.90 % 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: 2.95 (0.42), residues: 449 helix: 2.19 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.64 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 115 PHE 0.008 0.001 PHE A 355 TYR 0.009 0.001 TYR A 91 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7326 (ptt180) cc_final: 0.6936 (ptt90) REVERT: A 239 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: A 284 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6397 (mt-10) REVERT: A 431 ASN cc_start: 0.8036 (t0) cc_final: 0.7702 (t0) REVERT: A 435 MET cc_start: 0.8044 (tpp) cc_final: 0.7759 (tpp) REVERT: A 448 MET cc_start: 0.8327 (mmm) cc_final: 0.7969 (mmm) REVERT: A 472 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8087 (mm) REVERT: A 498 LEU cc_start: 0.7989 (tt) cc_final: 0.7431 (mm) outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.1330 time to fit residues: 14.3863 Evaluate side-chains 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3630 Z= 0.156 Angle : 0.598 12.457 4951 Z= 0.285 Chirality : 0.041 0.219 571 Planarity : 0.004 0.032 612 Dihedral : 4.177 36.956 516 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 17.77 % Favored : 79.84 % 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: 2.89 (0.42), residues: 449 helix: 2.16 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.58 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 115 PHE 0.008 0.001 PHE A 355 TYR 0.012 0.001 TYR A 72 ARG 0.002 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7344 (ptt180) cc_final: 0.6949 (ptt90) REVERT: A 122 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 239 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7679 (mpp) REVERT: A 284 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: A 431 ASN cc_start: 0.8033 (t0) cc_final: 0.7702 (t0) REVERT: A 435 MET cc_start: 0.8082 (tpp) cc_final: 0.7769 (tpp) REVERT: A 448 MET cc_start: 0.8316 (mmm) cc_final: 0.7952 (mmm) REVERT: A 472 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 498 LEU cc_start: 0.8028 (tt) cc_final: 0.7452 (mm) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1335 time to fit residues: 14.4802 Evaluate side-chains 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3630 Z= 0.199 Angle : 0.602 10.159 4951 Z= 0.289 Chirality : 0.041 0.217 571 Planarity : 0.004 0.033 612 Dihedral : 4.189 34.386 516 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.39 % Allowed : 18.04 % Favored : 79.58 % 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: 2.72 (0.41), residues: 449 helix: 2.06 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.40 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.016 0.001 TYR A 361 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 123 ASP cc_start: 0.8227 (m-30) cc_final: 0.7743 (m-30) REVERT: A 239 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7708 (mpp) REVERT: A 284 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: A 357 ASP cc_start: 0.8258 (m-30) cc_final: 0.7537 (m-30) REVERT: A 435 MET cc_start: 0.8143 (tpp) cc_final: 0.7852 (tpp) REVERT: A 448 MET cc_start: 0.8331 (mmm) cc_final: 0.7995 (mmm) REVERT: A 472 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 498 LEU cc_start: 0.8055 (tt) cc_final: 0.7469 (mm) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.1354 time to fit residues: 15.2228 Evaluate side-chains 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3630 Z= 0.166 Angle : 0.589 9.351 4951 Z= 0.284 Chirality : 0.040 0.214 571 Planarity : 0.004 0.029 612 Dihedral : 4.154 37.538 516 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.65 % Allowed : 17.24 % Favored : 80.11 % 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: 2.74 (0.41), residues: 449 helix: 2.09 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.37 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.002 0.000 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.013 0.001 TYR A 72 ARG 0.004 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7685 (mpp) REVERT: A 435 MET cc_start: 0.8127 (tpp) cc_final: 0.7829 (tpp) REVERT: A 448 MET cc_start: 0.8297 (mmm) cc_final: 0.7930 (mmm) REVERT: A 472 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 498 LEU cc_start: 0.8030 (tt) cc_final: 0.7455 (mm) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.1266 time to fit residues: 13.8145 Evaluate side-chains 88 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.188435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146723 restraints weight = 4713.725| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.64 r_work: 0.3488 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3630 Z= 0.218 Angle : 0.624 9.471 4951 Z= 0.306 Chirality : 0.042 0.311 571 Planarity : 0.004 0.032 612 Dihedral : 4.161 33.735 516 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.12 % Allowed : 18.83 % Favored : 79.05 % 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: 2.70 (0.41), residues: 449 helix: 2.04 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.42 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.015 0.001 TYR A 361 ARG 0.006 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1229.34 seconds wall clock time: 23 minutes 3.59 seconds (1383.59 seconds total)