Starting phenix.real_space_refine on Tue Feb 11 02:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc2_40335/02_2025/8sc2_40335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc2_40335/02_2025/8sc2_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_40335/02_2025/8sc2_40335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc2_40335/02_2025/8sc2_40335.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc2_40335/02_2025/8sc2_40335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc2_40335/02_2025/8sc2_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-5592/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: 2.90, per 1000 atoms: 0.82 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: 0.91 Conformation dependent library (CDL) restraints added in 607.2 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: 0.35 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: 1.04 Time building geometry restraints manager: 1.02 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: 0.010 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.550 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.1597 time to fit residues: 21.2097 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 : 0.392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149527 restraints weight = 4660.435| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.35 r_work: 0.3511 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7831 (t0) REVERT: A 431 ASN cc_start: 0.8123 (t0) cc_final: 0.7799 (t0) REVERT: A 435 MET cc_start: 0.8048 (tpp) cc_final: 0.7654 (tpp) REVERT: A 498 LEU cc_start: 0.7867 (tt) cc_final: 0.7408 (mm) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1294 time to fit residues: 15.2578 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 : 0.367 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.189029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148291 restraints weight = 4661.676| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.53 r_work: 0.3494 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2170 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= 0.206 Angle : 0.560 6.426 4951 Z= 0.279 Chirality : 0.040 0.184 571 Planarity : 0.004 0.031 612 Dihedral : 4.355 34.115 516 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 11.41 % Favored : 86.21 % 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: 2.77 (0.42), residues: 449 helix: 2.05 (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 0.008 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.010 0.001 PHE A 32 TYR 0.012 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 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 284 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6166 (mt-10) REVERT: A 435 MET cc_start: 0.8074 (tpp) cc_final: 0.7686 (tpp) REVERT: A 479 ILE cc_start: 0.6839 (mm) cc_final: 0.6579 (mt) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.1494 time to fit residues: 16.2534 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 : 0.372 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.3422 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.191478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150370 restraints weight = 4768.730| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.75 r_work: 0.3517 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3630 Z= 0.136 Angle : 0.510 9.218 4951 Z= 0.251 Chirality : 0.038 0.196 571 Planarity : 0.004 0.029 612 Dihedral : 4.226 35.498 516 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.39 % Allowed : 11.67 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.42), residues: 449 helix: 2.18 (0.31), residues: 313 sheet: None (None), residues: 0 loop : 1.54 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.001 0.000 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.012 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 93 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9090 (t0) cc_final: 0.8851 (t0) REVERT: A 122 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 431 ASN cc_start: 0.8070 (t0) cc_final: 0.7708 (t0) REVERT: A 435 MET cc_start: 0.7986 (tpp) cc_final: 0.7592 (tpp) REVERT: A 479 ILE cc_start: 0.6615 (mm) cc_final: 0.6411 (mt) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.1414 time to fit residues: 15.8017 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.190226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149553 restraints weight = 4805.160| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.62 r_work: 0.3505 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3630 Z= 0.172 Angle : 0.545 9.218 4951 Z= 0.263 Chirality : 0.039 0.203 571 Planarity : 0.004 0.031 612 Dihedral : 4.256 34.130 516 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.12 % Allowed : 12.47 % 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: 2.90 (0.42), residues: 449 helix: 2.17 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.55 (0.59), residues: 136 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 0.015 0.001 PHE A 334 TYR 0.008 0.001 TYR A 91 ARG 0.002 0.000 ARG A 486 *********************** 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 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7379 (ptt180) cc_final: 0.6916 (ptt90) REVERT: A 94 ASP cc_start: 0.9129 (t0) cc_final: 0.8866 (t0) REVERT: A 431 ASN cc_start: 0.8087 (t0) cc_final: 0.7750 (t0) REVERT: A 435 MET cc_start: 0.8028 (tpp) cc_final: 0.7641 (tpp) REVERT: A 498 LEU cc_start: 0.7889 (tt) cc_final: 0.7342 (mm) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.1494 time to fit residues: 16.1278 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 : 0.390 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 17 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.191202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149379 restraints weight = 4794.520| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.80 r_work: 0.3505 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2657 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= 0.148 Angle : 0.532 9.447 4951 Z= 0.255 Chirality : 0.040 0.272 571 Planarity : 0.004 0.031 612 Dihedral : 4.184 36.324 516 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.12 % Allowed : 14.59 % Favored : 83.29 % 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: 2.94 (0.42), residues: 449 helix: 2.23 (0.31), residues: 313 sheet: None (None), residues: 0 loop : 1.49 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.008 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 85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7350 (ptt180) cc_final: 0.6862 (ptt90) REVERT: A 94 ASP cc_start: 0.9146 (t0) cc_final: 0.8877 (t0) REVERT: A 431 ASN cc_start: 0.8088 (t0) cc_final: 0.7749 (t0) REVERT: A 435 MET cc_start: 0.8054 (tpp) cc_final: 0.7670 (tpp) REVERT: A 472 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 498 LEU cc_start: 0.7916 (tt) cc_final: 0.7345 (mm) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.1489 time to fit residues: 14.9745 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.190421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148307 restraints weight = 4716.694| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.76 r_work: 0.3491 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3630 Z= 0.179 Angle : 0.543 9.068 4951 Z= 0.262 Chirality : 0.039 0.234 571 Planarity : 0.004 0.031 612 Dihedral : 4.204 34.096 516 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.92 % Allowed : 13.79 % Favored : 83.29 % 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: 2.91 (0.42), residues: 449 helix: 2.19 (0.31), residues: 314 sheet: None (None), residues: 0 loop : 1.50 (0.59), residues: 135 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 0.015 0.001 TYR A 361 ARG 0.002 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 91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9171 (t0) cc_final: 0.8904 (t0) REVERT: A 123 ASP cc_start: 0.8302 (m-30) cc_final: 0.8060 (m-30) REVERT: A 239 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7784 (mpp) REVERT: A 431 ASN cc_start: 0.8115 (t0) cc_final: 0.7779 (t0) REVERT: A 435 MET cc_start: 0.8049 (tpp) cc_final: 0.7664 (tpp) REVERT: A 472 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 498 LEU cc_start: 0.7930 (tt) cc_final: 0.7336 (mm) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.1374 time to fit residues: 14.8814 Evaluate side-chains 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0030 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.190736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148726 restraints weight = 4739.630| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.40 r_work: 0.3506 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3630 Z= 0.160 Angle : 0.554 9.277 4951 Z= 0.268 Chirality : 0.039 0.220 571 Planarity : 0.004 0.031 612 Dihedral : 4.175 35.879 516 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.39 % Allowed : 16.71 % 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: 2.91 (0.42), residues: 449 helix: 2.21 (0.31), residues: 314 sheet: None (None), residues: 0 loop : 1.47 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.012 0.001 TYR A 72 ARG 0.004 0.000 ARG A 90 *********************** 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9173 (t0) cc_final: 0.8908 (t0) REVERT: A 239 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7745 (mpp) REVERT: A 431 ASN cc_start: 0.8080 (t0) cc_final: 0.7752 (t0) REVERT: A 435 MET cc_start: 0.8055 (tpp) cc_final: 0.7676 (tpp) REVERT: A 472 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 498 LEU cc_start: 0.7922 (tt) cc_final: 0.7326 (mm) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1381 time to fit residues: 14.1032 Evaluate side-chains 85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148999 restraints weight = 4663.315| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.65 r_work: 0.3500 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3630 Z= 0.177 Angle : 0.581 9.219 4951 Z= 0.282 Chirality : 0.040 0.213 571 Planarity : 0.004 0.031 612 Dihedral : 4.194 34.831 516 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.12 % Allowed : 17.77 % 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: 2.80 (0.42), residues: 449 helix: 2.12 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.46 (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 0.011 0.001 TYR A 91 ARG 0.002 0.000 ARG A 486 *********************** 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9171 (t0) cc_final: 0.8926 (t0) REVERT: A 239 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7748 (mpp) REVERT: A 431 ASN cc_start: 0.8081 (t0) cc_final: 0.7750 (t0) REVERT: A 435 MET cc_start: 0.8063 (tpp) cc_final: 0.7684 (tpp) REVERT: A 472 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (mm) REVERT: A 498 LEU cc_start: 0.7955 (tt) cc_final: 0.7353 (mm) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.1435 time to fit residues: 14.5565 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 : 0.370 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.189356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148093 restraints weight = 4693.040| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.57 r_work: 0.3491 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2882 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= 0.195 Angle : 0.586 9.476 4951 Z= 0.283 Chirality : 0.040 0.226 571 Planarity : 0.004 0.032 612 Dihedral : 4.169 32.418 516 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.65 % Allowed : 16.98 % Favored : 80.37 % 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: 2.77 (0.41), residues: 449 helix: 2.08 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.47 (0.58), residues: 135 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 0.010 0.001 PHE A 355 TYR 0.009 0.001 TYR A 352 ARG 0.002 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9177 (t0) cc_final: 0.8922 (t0) REVERT: A 239 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7779 (mpp) REVERT: A 435 MET cc_start: 0.8074 (tpp) cc_final: 0.7706 (tpp) REVERT: A 472 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8042 (mm) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 0.1449 time to fit residues: 14.8523 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.190587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148903 restraints weight = 4693.719| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.74 r_work: 0.3499 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3630 Z= 0.166 Angle : 0.594 9.781 4951 Z= 0.290 Chirality : 0.042 0.320 571 Planarity : 0.004 0.030 612 Dihedral : 4.183 34.719 516 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.86 % Allowed : 17.77 % Favored : 80.37 % 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: 2.78 (0.41), residues: 449 helix: 2.09 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.47 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.002 0.001 HIS A 115 PHE 0.009 0.001 PHE A 355 TYR 0.008 0.001 TYR A 404 ARG 0.002 0.000 ARG A 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.07 seconds wall clock time: 36 minutes 6.63 seconds (2166.63 seconds total)