Starting phenix.real_space_refine on Sat Apr 26 23:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc2_40335/04_2025/8sc2_40335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc2_40335/04_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_40335/04_2025/8sc2_40335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc2_40335/04_2025/8sc2_40335.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc2_40335/04_2025/8sc2_40335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc2_40335/04_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-5669/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: 2.72, per 1000 atoms: 0.77 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: 0.85 Conformation dependent library (CDL) restraints added in 393.1 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: 0.33 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: 0.88 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 637 1.33 - 1.45: 975 1.45 - 1.58: 1970 1.58 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 3630 Sorted by residual: bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.96e+00 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.19e+00 bond pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N LEU A 251 " pdb=" CA LEU A 251 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 bond pdb=" N TRP A 64 " pdb=" CA TRP A 64 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.24e-02 6.50e+03 5.82e+00 ... (remaining 3625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4713 1.07 - 2.14: 177 2.14 - 3.20: 44 3.20 - 4.27: 12 4.27 - 5.34: 5 Bond angle restraints: 4951 Sorted by residual: angle pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" O ILE A 365 " ideal model delta sigma weight residual 120.95 117.51 3.44 1.04e+00 9.25e-01 1.10e+01 angle pdb=" CA CYS A 36 " pdb=" C CYS A 36 " pdb=" O CYS A 36 " ideal model delta sigma weight residual 120.70 117.45 3.25 1.03e+00 9.43e-01 9.93e+00 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 120.57 117.59 2.98 1.07e+00 8.73e-01 7.78e+00 angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.49e+00 angle pdb=" N ASP A 149 " pdb=" CA ASP A 149 " pdb=" C ASP A 149 " ideal model delta sigma weight residual 111.71 108.79 2.92 1.15e+00 7.56e-01 6.43e+00 ... (remaining 4946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.24: 1889 9.24 - 18.49: 164 18.49 - 27.73: 47 27.73 - 36.98: 17 36.98 - 46.22: 6 Dihedral angle restraints: 2123 sinusoidal: 826 harmonic: 1297 Sorted by residual: dihedral pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" CB LEU A 192 " pdb=" CG LEU A 192 " ideal model delta sinusoidal sigma weight residual -60.00 -101.37 41.37 3 1.50e+01 4.44e-03 7.40e+00 dihedral pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" CB GLN A 241 " pdb=" CG GLN A 241 " ideal model delta sinusoidal sigma weight residual -180.00 -140.11 -39.89 3 1.50e+01 4.44e-03 7.09e+00 dihedral pdb=" C ILE A 365 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" CB ILE A 365 " ideal model delta harmonic sigma weight residual -122.00 -128.63 6.63 0 2.50e+00 1.60e-01 7.04e+00 ... (remaining 2120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 447 0.044 - 0.087: 93 0.087 - 0.130: 26 0.130 - 0.174: 3 0.174 - 0.217: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LEU A 248 " pdb=" N LEU A 248 " pdb=" C LEU A 248 " pdb=" CB LEU A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 35 " pdb=" CA ILE A 35 " pdb=" CG1 ILE A 35 " pdb=" CG2 ILE A 35 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 568 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C VAL A 40 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 40 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 196 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 258 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 259 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.016 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 839 2.79 - 3.31: 3487 3.31 - 3.84: 5626 3.84 - 4.37: 6374 4.37 - 4.90: 11282 Nonbonded interactions: 27608 Sorted by model distance: nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.258 3.040 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 3.040 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.297 3.040 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.317 3.040 nonbonded pdb=" O CYS A 142 " pdb=" OG SER A 145 " model vdw 2.360 3.040 ... (remaining 27603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 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 : 8.521 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 Details of bonding type rmsd hydrogen bonds : bond 0.14429 ( 240) hydrogen bonds : angle 5.37936 ( 699) SS BOND : bond 0.00184 ( 3) SS BOND : angle 1.63468 ( 6) covalent geometry : bond 0.00315 ( 3630) covalent geometry : angle 0.55146 ( 4951) *********************** 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 : 0.338 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: 0.1555 time to fit residues: 20.7179 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 : 0.375 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.191320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149792 restraints weight = 4658.255| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.36 r_work: 0.3515 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.026 3633 Z= 0.134 Angle : 0.575 7.855 4957 Z= 0.288 Chirality : 0.040 0.214 571 Planarity : 0.004 0.037 612 Dihedral : 4.259 28.934 516 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 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 240) hydrogen bonds : angle 4.26518 ( 699) SS BOND : bond 0.00118 ( 3) SS BOND : angle 2.11601 ( 6) covalent geometry : bond 0.00296 ( 3630) covalent geometry : angle 0.57101 ( 4951) *********************** 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 : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 431 ASN cc_start: 0.8124 (t0) cc_final: 0.7797 (t0) REVERT: A 435 MET cc_start: 0.8071 (tpp) cc_final: 0.7672 (tpp) REVERT: A 498 LEU cc_start: 0.7857 (tt) cc_final: 0.7401 (mm) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1264 time to fit residues: 14.8705 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 : 0.360 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.189184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148441 restraints weight = 4662.482| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.54 r_work: 0.3497 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2179 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= 0.132 Angle : 0.561 6.427 4957 Z= 0.279 Chirality : 0.040 0.181 571 Planarity : 0.004 0.031 612 Dihedral : 4.364 34.969 516 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 10.88 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (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 0.013 0.001 TYR A 72 ARG 0.004 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 240) hydrogen bonds : angle 4.14498 ( 699) SS BOND : bond 0.00217 ( 3) SS BOND : angle 1.88896 ( 6) covalent geometry : bond 0.00299 ( 3630) covalent geometry : angle 0.55760 ( 4951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 284 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: A 431 ASN cc_start: 0.8143 (t0) cc_final: 0.7801 (t0) REVERT: A 435 MET cc_start: 0.8064 (tpp) cc_final: 0.7666 (tpp) REVERT: A 479 ILE cc_start: 0.6827 (mm) cc_final: 0.6568 (mt) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1433 time to fit residues: 15.8850 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.190985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150306 restraints weight = 4758.756| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.58 r_work: 0.3522 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3633 Z= 0.106 Angle : 0.520 9.118 4957 Z= 0.257 Chirality : 0.038 0.194 571 Planarity : 0.004 0.029 612 Dihedral : 4.337 36.288 516 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.65 % Allowed : 11.67 % Favored : 85.68 % 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: 2.87 (0.42), residues: 449 helix: 2.15 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.56 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.002 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 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 240) hydrogen bonds : angle 3.99120 ( 699) SS BOND : bond 0.00173 ( 3) SS BOND : angle 1.66808 ( 6) covalent geometry : bond 0.00221 ( 3630) covalent geometry : angle 0.51730 ( 4951) *********************** 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 91 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9059 (t0) cc_final: 0.8833 (t0) REVERT: A 122 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 431 ASN cc_start: 0.8050 (t0) cc_final: 0.7703 (t0) REVERT: A 435 MET cc_start: 0.8021 (tpp) cc_final: 0.7615 (tpp) REVERT: A 448 MET cc_start: 0.8459 (mmm) cc_final: 0.8034 (mmm) REVERT: A 479 ILE cc_start: 0.6714 (mm) cc_final: 0.6494 (mt) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.1233 time to fit residues: 13.9678 Evaluate side-chains 81 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.190487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150066 restraints weight = 4777.558| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.56 r_work: 0.3515 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3633 Z= 0.110 Angle : 0.545 9.279 4957 Z= 0.262 Chirality : 0.039 0.205 571 Planarity : 0.004 0.031 612 Dihedral : 4.262 34.592 516 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.39 % Allowed : 12.73 % 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 (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 (0.30), residues: 313 sheet: None (None), residues: 0 loop : 1.55 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.015 0.001 PHE A 334 TYR 0.009 0.001 TYR A 91 ARG 0.003 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 240) hydrogen bonds : angle 3.99095 ( 699) SS BOND : bond 0.00192 ( 3) SS BOND : angle 1.68593 ( 6) covalent geometry : bond 0.00243 ( 3630) covalent geometry : angle 0.54230 ( 4951) *********************** 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: 9 poor density : 81 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7390 (ptt180) cc_final: 0.6913 (ptt90) REVERT: A 94 ASP cc_start: 0.9122 (t0) cc_final: 0.8874 (t0) REVERT: A 431 ASN cc_start: 0.8105 (t0) cc_final: 0.7775 (t0) REVERT: A 435 MET cc_start: 0.8002 (tpp) cc_final: 0.7636 (tpp) REVERT: A 448 MET cc_start: 0.8468 (mmm) cc_final: 0.8062 (mmm) REVERT: A 498 LEU cc_start: 0.7875 (tt) cc_final: 0.7318 (mm) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.1466 time to fit residues: 15.8467 Evaluate side-chains 85 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.190501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149456 restraints weight = 4785.100| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.61 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: 0.8004 moved from start: 0.2675 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= 0.121 Angle : 0.564 9.317 4957 Z= 0.273 Chirality : 0.041 0.271 571 Planarity : 0.004 0.031 612 Dihedral : 4.246 33.799 516 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.65 % Allowed : 15.65 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.42), residues: 449 helix: 2.09 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.57 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.013 0.001 TYR A 72 ARG 0.002 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 240) hydrogen bonds : angle 4.05262 ( 699) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.71014 ( 6) covalent geometry : bond 0.00276 ( 3630) covalent geometry : angle 0.56160 ( 4951) *********************** 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 87 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7419 (ptt180) cc_final: 0.6935 (ptt90) REVERT: A 94 ASP cc_start: 0.9142 (t0) cc_final: 0.8886 (t0) REVERT: A 435 MET cc_start: 0.8053 (tpp) cc_final: 0.7671 (tpp) REVERT: A 448 MET cc_start: 0.8501 (mmm) cc_final: 0.8069 (mmm) REVERT: A 472 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8062 (mm) REVERT: A 498 LEU cc_start: 0.7923 (tt) cc_final: 0.7349 (mm) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.1513 time to fit residues: 15.7149 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 : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 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: 0.6980 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.190293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149122 restraints weight = 4707.981| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.57 r_work: 0.3502 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3633 Z= 0.114 Angle : 0.558 9.154 4957 Z= 0.268 Chirality : 0.040 0.233 571 Planarity : 0.004 0.031 612 Dihedral : 4.180 34.730 516 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.92 % Allowed : 16.45 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.42), residues: 449 helix: 2.17 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.55 (0.59), 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 115 PHE 0.009 0.001 PHE A 355 TYR 0.008 0.001 TYR A 91 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 240) hydrogen bonds : angle 4.03577 ( 699) SS BOND : bond 0.00198 ( 3) SS BOND : angle 1.67672 ( 6) covalent geometry : bond 0.00258 ( 3630) covalent geometry : angle 0.55512 ( 4951) *********************** 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 84 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7445 (ptt180) cc_final: 0.7051 (ptt90) REVERT: A 94 ASP cc_start: 0.9174 (t0) cc_final: 0.8907 (t0) REVERT: A 239 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7756 (mpp) REVERT: A 435 MET cc_start: 0.8036 (tpp) cc_final: 0.7688 (tpp) REVERT: A 448 MET cc_start: 0.8474 (mmm) cc_final: 0.8035 (mmm) REVERT: A 472 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8066 (mm) REVERT: A 498 LEU cc_start: 0.7926 (tt) cc_final: 0.7331 (mm) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.1288 time to fit residues: 13.0755 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 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 = 0.4133 r_free = 0.4133 target = 0.188964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147999 restraints weight = 4725.249| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.59 r_work: 0.3493 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2798 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= 0.128 Angle : 0.573 9.324 4957 Z= 0.276 Chirality : 0.040 0.217 571 Planarity : 0.004 0.032 612 Dihedral : 4.226 31.977 516 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.39 % Allowed : 16.18 % Favored : 81.43 % 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: 2.85 (0.41), residues: 449 helix: 2.14 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.51 (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 0.012 0.001 TYR A 72 ARG 0.001 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 240) hydrogen bonds : angle 4.09448 ( 699) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.73179 ( 6) covalent geometry : bond 0.00298 ( 3630) covalent geometry : angle 0.57028 ( 4951) *********************** 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: 9 poor density : 77 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9181 (t0) cc_final: 0.8931 (t0) REVERT: A 239 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7770 (mpp) REVERT: A 435 MET cc_start: 0.8045 (tpp) cc_final: 0.7702 (tpp) REVERT: A 448 MET cc_start: 0.8456 (mmm) cc_final: 0.8015 (mmm) REVERT: A 472 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 498 LEU cc_start: 0.7955 (tt) cc_final: 0.7364 (mm) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1332 time to fit residues: 13.7806 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 : 0.345 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.188385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146981 restraints weight = 4701.378| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.58 r_work: 0.3490 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2877 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= 0.126 Angle : 0.575 9.355 4957 Z= 0.277 Chirality : 0.040 0.221 571 Planarity : 0.004 0.032 612 Dihedral : 4.185 32.150 516 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.39 % Allowed : 16.45 % 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 (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: 2.82 (0.41), residues: 449 helix: 2.11 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.50 (0.59), 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 0.005 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 240) hydrogen bonds : angle 4.09096 ( 699) SS BOND : bond 0.00204 ( 3) SS BOND : angle 1.80488 ( 6) covalent geometry : bond 0.00291 ( 3630) covalent geometry : angle 0.57217 ( 4951) *********************** 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 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9189 (t0) cc_final: 0.8935 (t0) REVERT: A 239 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7788 (mpp) REVERT: A 435 MET cc_start: 0.8033 (tpp) cc_final: 0.7676 (tpp) REVERT: A 448 MET cc_start: 0.8476 (mmm) cc_final: 0.7988 (mmm) REVERT: A 472 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8031 (mm) REVERT: A 498 LEU cc_start: 0.7961 (tt) cc_final: 0.7368 (mm) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1461 time to fit residues: 14.8384 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 : 0.373 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 0.0270 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.190950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149607 restraints weight = 4724.172| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.73 r_work: 0.3510 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3633 Z= 0.109 Angle : 0.569 9.705 4957 Z= 0.274 Chirality : 0.039 0.220 571 Planarity : 0.004 0.032 612 Dihedral : 4.175 35.663 516 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.86 % Allowed : 17.51 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.41), residues: 449 helix: 2.19 (0.30), residues: 311 sheet: None (None), residues: 0 loop : 1.63 (0.58), residues: 138 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 0.008 0.001 PHE A 355 TYR 0.006 0.001 TYR A 352 ARG 0.006 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 240) hydrogen bonds : angle 4.03619 ( 699) SS BOND : bond 0.00183 ( 3) SS BOND : angle 1.70546 ( 6) covalent geometry : bond 0.00238 ( 3630) covalent geometry : angle 0.56645 ( 4951) ********************** 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 86 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.9186 (t0) cc_final: 0.8933 (t0) REVERT: A 113 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.7382 (ttt-90) REVERT: A 239 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7785 (mpp) REVERT: A 435 MET cc_start: 0.8048 (tpp) cc_final: 0.7688 (tpp) REVERT: A 448 MET cc_start: 0.8465 (mmm) cc_final: 0.8013 (mmm) REVERT: A 472 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 498 LEU cc_start: 0.7933 (tt) cc_final: 0.7339 (mm) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.1252 time to fit residues: 12.7120 Evaluate side-chains 82 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 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 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 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 = 0.4135 r_free = 0.4135 target = 0.189249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147744 restraints weight = 4730.343| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.67 r_work: 0.3495 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3039 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= 0.137 Angle : 0.614 9.481 4957 Z= 0.305 Chirality : 0.042 0.312 571 Planarity : 0.004 0.038 612 Dihedral : 4.169 32.513 516 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 19.10 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.41), residues: 449 helix: 2.10 (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 115 PHE 0.010 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.006 0.001 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 240) hydrogen bonds : angle 4.10590 ( 699) SS BOND : bond 0.00203 ( 3) SS BOND : angle 1.75021 ( 6) covalent geometry : bond 0.00316 ( 3630) covalent geometry : angle 0.61180 ( 4951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.72 seconds wall clock time: 36 minutes 53.81 seconds (2213.81 seconds total)