Starting phenix.real_space_refine on Wed Jul 1 22:46:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sc2_40335/07_2026/8sc2_40335.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 0.83, per 1000 atoms: 0.23 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: 0.20 Conformation dependent library (CDL) restraints added in 87.5 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: 0.10 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: 0.37 Time building geometry restraints manager: 0.25 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: 1869 9.24 - 18.49: 163 18.49 - 27.73: 44 27.73 - 36.98: 17 36.98 - 46.22: 6 Dihedral angle restraints: 2099 sinusoidal: 802 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 2096 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.820 Find NCS groups from input model: 0.010 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 3633 Z= 0.201 Angle : 0.554 5.341 4957 Z= 0.346 Chirality : 0.041 0.217 571 Planarity : 0.004 0.036 612 Dihedral : 8.528 46.221 1260 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 462 TYR 0.007 0.001 TYR A 168 PHE 0.009 0.001 PHE A 355 TRP 0.010 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.20 ( 3630) covalent geometry : angle 0.55146 / 0.35 ( 4951) SS BOND : bond 0.00184 / 0.10 ( 3) SS BOND : angle 1.63468 / 0.85 ( 6) hydrogen bonds : bond 0.14429 / 9.29 ( 240) hydrogen bonds : angle 5.37936 / 3.76 ( 699) *********************** 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 : 0.134 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: 0.0562 time to fit residues: 7.6393 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4146 r_free = 0.4146 target = 0.191156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151248 restraints weight = 4799.866| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.49 r_work: 0.3511 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3633 Z= 0.136 Angle : 0.576 7.760 4957 Z= 0.288 Chirality : 0.040 0.209 571 Planarity : 0.004 0.038 612 Dihedral : 4.037 25.629 492 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.59 % Allowed : 9.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.42), residues: 449 helix: 2.10 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.66 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 486 TYR 0.013 0.001 TYR A 72 PHE 0.015 0.001 PHE A 334 TRP 0.009 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 3630) covalent geometry : angle 0.57112 / 0.29 ( 4951) SS BOND : bond 0.00149 / 0.08 ( 3) SS BOND : angle 2.13610 / 1.15 ( 6) hydrogen bonds : bond 0.04266 / 2.78 ( 240) hydrogen bonds : angle 4.27325 / 3.00 ( 699) *********************** 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 94 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8045 (tpp) cc_final: 0.7665 (tpp) REVERT: A 498 LEU cc_start: 0.7864 (tt) cc_final: 0.7407 (mm) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 0.0453 time to fit residues: 5.2975 Evaluate side-chains 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU 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 25 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148530 restraints weight = 4735.844| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.54 r_work: 0.3498 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3633 Z= 0.129 Angle : 0.560 6.488 4957 Z= 0.279 Chirality : 0.040 0.179 571 Planarity : 0.004 0.031 612 Dihedral : 4.188 33.560 492 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.42), residues: 449 helix: 2.04 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.57 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.013 0.001 TYR A 72 PHE 0.010 0.001 PHE A 32 TRP 0.007 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3630) covalent geometry : angle 0.55605 / 0.28 ( 4951) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 1.90011 / 1.01 ( 6) hydrogen bonds : bond 0.03946 / 2.60 ( 240) hydrogen bonds : angle 4.13748 / 2.93 ( 699) *********************** 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 92 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 284 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6160 (mt-10) REVERT: A 431 ASN cc_start: 0.8136 (t0) cc_final: 0.7796 (t0) REVERT: A 435 MET cc_start: 0.8065 (tpp) cc_final: 0.7664 (tpp) REVERT: A 479 ILE cc_start: 0.6819 (mm) cc_final: 0.6559 (mt) REVERT: A 504 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7516 (mm) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.0392 time to fit residues: 4.5223 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 : 0.111 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.188284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146301 restraints weight = 4760.353| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.62 r_work: 0.3474 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3633 Z= 0.148 Angle : 0.564 8.849 4957 Z= 0.280 Chirality : 0.040 0.193 571 Planarity : 0.004 0.034 612 Dihedral : 4.127 28.499 492 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.65 % Allowed : 12.47 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.42), residues: 449 helix: 2.00 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.49 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.011 0.001 TYR A 72 PHE 0.011 0.001 PHE A 32 TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 3630) covalent geometry : angle 0.56048 / 0.28 ( 4951) SS BOND : bond 0.00345 / 0.18 ( 3) SS BOND : angle 1.95948 / 1.02 ( 6) hydrogen bonds : bond 0.04013 / 2.65 ( 240) hydrogen bonds : angle 4.19974 / 2.98 ( 699) *********************** 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 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7451 (ptt180) cc_final: 0.7081 (ptt90) REVERT: A 122 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 284 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6187 (mt-10) REVERT: A 435 MET cc_start: 0.8074 (tpp) cc_final: 0.7686 (tpp) REVERT: A 448 MET cc_start: 0.8529 (mmm) cc_final: 0.8100 (mmm) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.0466 time to fit residues: 5.3346 Evaluate side-chains 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147778 restraints weight = 4729.969| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.56 r_work: 0.3486 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3633 Z= 0.131 Angle : 0.573 8.965 4957 Z= 0.276 Chirality : 0.039 0.199 571 Planarity : 0.004 0.031 612 Dihedral : 4.056 24.537 492 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.45 % Allowed : 12.20 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.42), residues: 449 helix: 2.02 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.52 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.012 0.001 TYR A 72 PHE 0.015 0.001 PHE A 334 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3630) covalent geometry : angle 0.56973 / 0.27 ( 4951) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 1.81463 / 0.95 ( 6) hydrogen bonds : bond 0.03789 / 2.50 ( 240) hydrogen bonds : angle 4.12072 / 2.93 ( 699) *********************** 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 95 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7443 (ptt180) cc_final: 0.7070 (ptt90) REVERT: A 122 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 435 MET cc_start: 0.8006 (tpp) cc_final: 0.7650 (tpp) REVERT: A 448 MET cc_start: 0.8510 (mmm) cc_final: 0.8091 (mmm) REVERT: A 472 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 479 ILE cc_start: 0.6868 (mm) cc_final: 0.6636 (mt) REVERT: A 498 LEU cc_start: 0.7916 (tt) cc_final: 0.7337 (mm) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 0.0452 time to fit residues: 5.1435 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 : 0.101 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146959 restraints weight = 4715.313| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.55 r_work: 0.3470 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3633 Z= 0.146 Angle : 0.594 9.007 4957 Z= 0.290 Chirality : 0.042 0.272 571 Planarity : 0.004 0.033 612 Dihedral : 4.104 26.333 492 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.92 % Allowed : 15.12 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.42), residues: 449 helix: 1.95 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.51 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.016 0.001 TYR A 72 PHE 0.010 0.001 PHE A 355 TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3630) covalent geometry : angle 0.59045 / 0.29 ( 4951) SS BOND : bond 0.00250 / 0.13 ( 3) SS BOND : angle 1.84614 / 0.97 ( 6) hydrogen bonds : bond 0.03931 / 2.61 ( 240) hydrogen bonds : angle 4.21336 / 2.99 ( 699) *********************** 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 89 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8302 (m-30) cc_final: 0.8082 (m-30) REVERT: A 435 MET cc_start: 0.8027 (tpp) cc_final: 0.7665 (tpp) REVERT: A 448 MET cc_start: 0.8505 (mmm) cc_final: 0.8063 (mmm) REVERT: A 472 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 498 LEU cc_start: 0.7901 (tt) cc_final: 0.7312 (mm) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.0506 time to fit residues: 5.3171 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 : 0.119 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146275 restraints weight = 4729.224| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.61 r_work: 0.3482 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3633 Z= 0.130 Angle : 0.585 9.020 4957 Z= 0.282 Chirality : 0.041 0.231 571 Planarity : 0.004 0.032 612 Dihedral : 4.070 25.117 492 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.92 % Allowed : 15.92 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.42), residues: 449 helix: 2.04 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.50 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.013 0.001 TYR A 72 PHE 0.009 0.001 PHE A 355 TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3630) covalent geometry : angle 0.58205 / 0.28 ( 4951) SS BOND : bond 0.00210 / 0.11 ( 3) SS BOND : angle 1.81771 / 0.95 ( 6) hydrogen bonds : bond 0.03765 / 2.49 ( 240) hydrogen bonds : angle 4.16303 / 2.96 ( 699) *********************** 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7815 (mpp) REVERT: A 435 MET cc_start: 0.8010 (tpp) cc_final: 0.7666 (tpp) REVERT: A 448 MET cc_start: 0.8473 (mmm) cc_final: 0.8026 (mmm) REVERT: A 472 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 479 ILE cc_start: 0.6914 (mm) cc_final: 0.6674 (mt) REVERT: A 498 LEU cc_start: 0.7948 (tt) cc_final: 0.7364 (mm) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.0437 time to fit residues: 4.5806 Evaluate side-chains 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148291 restraints weight = 4807.165| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.59 r_work: 0.3491 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3633 Z= 0.120 Angle : 0.605 10.944 4957 Z= 0.292 Chirality : 0.041 0.224 571 Planarity : 0.004 0.032 612 Dihedral : 4.080 27.853 492 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.92 % Allowed : 16.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.42), residues: 449 helix: 2.06 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.55 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.011 0.001 TYR A 91 PHE 0.009 0.001 PHE A 355 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3630) covalent geometry : angle 0.60240 / 0.29 ( 4951) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 1.71609 / 0.90 ( 6) hydrogen bonds : bond 0.03616 / 2.38 ( 240) hydrogen bonds : angle 4.20681 / 2.98 ( 699) *********************** 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 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: A 404 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 435 MET cc_start: 0.8017 (tpp) cc_final: 0.7662 (tpp) REVERT: A 448 MET cc_start: 0.8478 (mmm) cc_final: 0.8028 (mmm) REVERT: A 472 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8004 (mm) REVERT: A 479 ILE cc_start: 0.6824 (mm) cc_final: 0.6590 (mt) REVERT: A 498 LEU cc_start: 0.7949 (tt) cc_final: 0.7351 (mm) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.0570 time to fit residues: 5.6818 Evaluate side-chains 85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 404 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.187057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145419 restraints weight = 4700.115| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.58 r_work: 0.3477 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3633 Z= 0.140 Angle : 0.624 11.175 4957 Z= 0.301 Chirality : 0.041 0.221 571 Planarity : 0.004 0.033 612 Dihedral : 4.039 25.156 492 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.39 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.42), residues: 449 helix: 1.98 (0.30), residues: 314 sheet: -0.58 (1.40), residues: 10 loop : 1.60 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.011 0.001 TYR A 72 PHE 0.010 0.001 PHE A 355 TRP 0.010 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3630) covalent geometry : angle 0.62143 / 0.30 ( 4951) SS BOND : bond 0.00224 / 0.11 ( 3) SS BOND : angle 1.81293 / 0.95 ( 6) hydrogen bonds : bond 0.03817 / 2.52 ( 240) hydrogen bonds : angle 4.25517 / 3.01 ( 699) *********************** 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 83 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: A 435 MET cc_start: 0.8076 (tpp) cc_final: 0.7717 (tpp) REVERT: A 448 MET cc_start: 0.8474 (mmm) cc_final: 0.8015 (mmm) REVERT: A 472 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8022 (mm) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.0351 time to fit residues: 3.6425 Evaluate side-chains 82 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148338 restraints weight = 4838.822| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.59 r_work: 0.3510 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3633 Z= 0.109 Angle : 0.596 10.249 4957 Z= 0.287 Chirality : 0.040 0.220 571 Planarity : 0.004 0.031 612 Dihedral : 3.973 30.779 492 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.39 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.42), residues: 449 helix: 2.12 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.64 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.007 0.001 TYR A 361 PHE 0.007 0.001 PHE A 355 TRP 0.008 0.001 TRP A 354 HIS 0.002 0.000 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 3630) covalent geometry : angle 0.59362 / 0.29 ( 4951) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 1.62371 / 0.85 ( 6) hydrogen bonds : bond 0.03384 / 2.22 ( 240) hydrogen bonds : angle 4.10377 / 2.91 ( 699) ********************** 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 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7730 (mpp) REVERT: A 435 MET cc_start: 0.7975 (tpp) cc_final: 0.7640 (tpp) REVERT: A 448 MET cc_start: 0.8403 (mmm) cc_final: 0.7898 (mmm) REVERT: A 472 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8077 (mm) REVERT: A 479 ILE cc_start: 0.6772 (mm) cc_final: 0.6555 (mt) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.0387 time to fit residues: 4.0220 Evaluate side-chains 80 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 37 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149586 restraints weight = 4741.449| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.67 r_work: 0.3508 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3633 Z= 0.115 Angle : 0.624 9.745 4957 Z= 0.307 Chirality : 0.043 0.313 571 Planarity : 0.004 0.042 612 Dihedral : 3.986 31.257 492 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.39 % Allowed : 18.30 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.42), residues: 449 helix: 2.14 (0.31), residues: 313 sheet: None (None), residues: 0 loop : 1.38 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 344 TYR 0.012 0.001 TYR A 72 PHE 0.008 0.001 PHE A 355 TRP 0.008 0.001 TRP A 354 HIS 0.002 0.000 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3630) covalent geometry : angle 0.62161 / 0.31 ( 4951) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 1.62315 / 0.85 ( 6) hydrogen bonds : bond 0.03512 / 2.27 ( 240) hydrogen bonds : angle 4.08106 / 2.87 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 810.87 seconds wall clock time: 14 minutes 28.08 seconds (868.08 seconds total)