Starting phenix.real_space_refine on Sun Apr 27 00:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjq_37589/04_2025/8wjq_37589.cif" } resolution = 3.8 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= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2599 2.51 5 N 676 2.21 5 O 694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 3999 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3987 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 29, 'TRANS': 500} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.71 Number of scatterers: 3999 At special positions: 0 Unit cell: (107, 85.6, 67.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 694 8.00 N 676 7.00 C 2599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 481.1 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 83.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 14 through 41 removed outlier: 3.526A pdb=" N VAL A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.802A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.519A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 255 Processing helix chain 'A' and resid 257 through 277 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.662A pdb=" N THR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 4.309A pdb=" N GLU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.512A pdb=" N LEU A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 Processing helix chain 'A' and resid 369 through 375 removed outlier: 3.574A pdb=" N GLY A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.756A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.046A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 490 removed outlier: 4.356A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.613A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.603A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.737A pdb=" N ARG A 48 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 308 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 620 1.32 - 1.45: 1117 1.45 - 1.58: 2311 1.58 - 1.71: 3 1.71 - 1.84: 48 Bond restraints: 4099 Sorted by residual: bond pdb=" CG PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.24e+01 bond pdb=" CG PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.503 1.280 0.223 3.40e-02 8.65e+02 4.30e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.479 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.464 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 4094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 5450 3.91 - 7.81: 115 7.81 - 11.72: 28 11.72 - 15.62: 6 15.62 - 19.53: 2 Bond angle restraints: 5601 Sorted by residual: angle pdb=" CA PRO A 146 " pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 112.00 92.47 19.53 1.40e+00 5.10e-01 1.95e+02 angle pdb=" CA PRO A 194 " pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 112.00 94.02 17.98 1.40e+00 5.10e-01 1.65e+02 angle pdb=" N PRO A 146 " pdb=" CD PRO A 146 " pdb=" CG PRO A 146 " ideal model delta sigma weight residual 103.20 90.41 12.79 1.50e+00 4.44e-01 7.27e+01 angle pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " ideal model delta sigma weight residual 114.10 129.04 -14.94 2.00e+00 2.50e-01 5.58e+01 angle pdb=" N PRO A 194 " pdb=" CD PRO A 194 " pdb=" CG PRO A 194 " ideal model delta sigma weight residual 103.20 92.88 10.32 1.50e+00 4.44e-01 4.74e+01 ... (remaining 5596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 2110 16.85 - 33.70: 188 33.70 - 50.55: 80 50.55 - 67.40: 13 67.40 - 84.25: 2 Dihedral angle restraints: 2393 sinusoidal: 885 harmonic: 1508 Sorted by residual: dihedral pdb=" CA MET A 36 " pdb=" C MET A 36 " pdb=" N LEU A 37 " pdb=" CA LEU A 37 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 137.60 -44.60 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" N ARG A 92 " pdb=" C ARG A 92 " pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " ideal model delta harmonic sigma weight residual 122.80 135.35 -12.55 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 2390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 583 0.099 - 0.198: 70 0.198 - 0.296: 6 0.296 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 661 Sorted by residual: chirality pdb=" CB THR A 453 " pdb=" CA THR A 453 " pdb=" OG1 THR A 453 " pdb=" CG2 THR A 453 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ARG A 92 " pdb=" N ARG A 92 " pdb=" C ARG A 92 " pdb=" CB ARG A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA THR A 453 " pdb=" N THR A 453 " pdb=" C THR A 453 " pdb=" CB THR A 453 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 658 not shown) Planarity restraints: 697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 193 " -0.150 5.00e-02 4.00e+02 2.07e-01 6.89e+01 pdb=" N PRO A 194 " 0.358 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " -0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 145 " 0.135 5.00e-02 4.00e+02 1.84e-01 5.43e+01 pdb=" N PRO A 146 " -0.318 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " 0.048 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" CG TRP A 135 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " 0.006 2.00e-02 2.50e+03 ... (remaining 694 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 443 2.75 - 3.29: 4171 3.29 - 3.83: 6912 3.83 - 4.36: 7162 4.36 - 4.90: 12407 Nonbonded interactions: 31095 Sorted by model distance: nonbonded pdb=" O ALA A 359 " pdb=" OG1 THR A 363 " model vdw 2.216 3.040 nonbonded pdb=" O LEU A 221 " pdb=" OG1 THR A 225 " model vdw 2.253 3.040 nonbonded pdb=" O SER A 336 " pdb=" OG1 THR A 339 " model vdw 2.275 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.275 3.040 nonbonded pdb=" O TRP A 50 " pdb=" NH1 ARG A 90 " model vdw 2.284 3.120 ... (remaining 31090 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 group one per residue 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.010 0.269 4101 Z= 0.420 Angle : 1.471 19.530 5605 Z= 0.789 Chirality : 0.066 0.494 661 Planarity : 0.018 0.207 697 Dihedral : 15.618 84.254 1415 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.48 % Allowed : 16.67 % Favored : 82.85 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 526 helix: 0.97 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -0.79 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.004 TRP A 135 HIS 0.016 0.003 HIS A 47 PHE 0.036 0.004 PHE A 348 TYR 0.027 0.006 TYR A 275 ARG 0.044 0.004 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.12570 ( 308) hydrogen bonds : angle 5.82813 ( 888) SS BOND : bond 0.00812 ( 2) SS BOND : angle 2.30303 ( 4) covalent geometry : bond 0.00983 ( 4099) covalent geometry : angle 1.47004 ( 5601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.5901 (tpt) cc_final: 0.5642 (tpt) REVERT: A 324 MET cc_start: 0.6727 (mmm) cc_final: 0.6518 (mmm) REVERT: A 466 MET cc_start: 0.6760 (mmp) cc_final: 0.6249 (mmm) REVERT: A 531 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6813 (tm-30) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.1394 time to fit residues: 13.3854 Evaluate side-chains 68 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 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 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.261681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.218600 restraints weight = 4807.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.225070 restraints weight = 2694.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.229468 restraints weight = 1783.104| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4101 Z= 0.168 Angle : 0.709 9.784 5605 Z= 0.363 Chirality : 0.041 0.173 661 Planarity : 0.008 0.097 697 Dihedral : 4.319 16.853 561 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.14 % Allowed : 17.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.37), residues: 526 helix: 1.51 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.42 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 135 HIS 0.006 0.001 HIS A 86 PHE 0.017 0.002 PHE A 269 TYR 0.021 0.002 TYR A 275 ARG 0.004 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.06167 ( 308) hydrogen bonds : angle 4.79821 ( 888) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.54761 ( 4) covalent geometry : bond 0.00344 ( 4099) covalent geometry : angle 0.70843 ( 5601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.424 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 0.1245 time to fit residues: 14.2881 Evaluate side-chains 69 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 7 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.272344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.227500 restraints weight = 4769.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.234201 restraints weight = 2618.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.239038 restraints weight = 1723.523| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4101 Z= 0.155 Angle : 0.676 11.629 5605 Z= 0.333 Chirality : 0.040 0.158 661 Planarity : 0.006 0.063 697 Dihedral : 4.258 15.037 561 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 19.08 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.37), residues: 526 helix: 1.65 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 135 HIS 0.005 0.001 HIS A 86 PHE 0.034 0.002 PHE A 269 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05773 ( 308) hydrogen bonds : angle 4.52218 ( 888) SS BOND : bond 0.00842 ( 2) SS BOND : angle 2.24050 ( 4) covalent geometry : bond 0.00297 ( 4099) covalent geometry : angle 0.67401 ( 5601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7378 (tp-100) cc_final: 0.6946 (tp-100) REVERT: A 120 TRP cc_start: 0.7040 (m-90) cc_final: 0.6550 (m-90) REVERT: A 324 MET cc_start: 0.6585 (mmm) cc_final: 0.6111 (mmm) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1396 time to fit residues: 13.3887 Evaluate side-chains 66 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.251556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.202053 restraints weight = 4785.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.208746 restraints weight = 2636.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.213330 restraints weight = 1750.450| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4101 Z= 0.193 Angle : 0.691 11.277 5605 Z= 0.348 Chirality : 0.041 0.148 661 Planarity : 0.006 0.064 697 Dihedral : 4.298 18.372 561 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.90 % Allowed : 23.19 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.37), residues: 526 helix: 1.48 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.72 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 357 HIS 0.004 0.001 HIS A 86 PHE 0.027 0.002 PHE A 269 TYR 0.016 0.003 TYR A 275 ARG 0.004 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.06471 ( 308) hydrogen bonds : angle 4.79877 ( 888) SS BOND : bond 0.00441 ( 2) SS BOND : angle 1.35102 ( 4) covalent geometry : bond 0.00411 ( 4099) covalent geometry : angle 0.69070 ( 5601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.5529 (mmp) cc_final: 0.5172 (mmp) REVERT: A 95 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7422 (tp40) REVERT: A 284 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.6300 (ttm-80) REVERT: A 324 MET cc_start: 0.6667 (mmm) cc_final: 0.6410 (mmm) REVERT: A 394 MET cc_start: 0.5856 (mmt) cc_final: 0.5563 (mmp) REVERT: A 453 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6534 (m) outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.1462 time to fit residues: 15.0173 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.0020 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.248143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201738 restraints weight = 4938.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.208032 restraints weight = 2802.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.212209 restraints weight = 1891.589| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4101 Z= 0.147 Angle : 0.639 11.419 5605 Z= 0.313 Chirality : 0.039 0.121 661 Planarity : 0.005 0.055 697 Dihedral : 4.258 16.532 561 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.14 % Allowed : 23.91 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.37), residues: 526 helix: 1.79 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.66 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 120 HIS 0.002 0.000 HIS A 47 PHE 0.015 0.001 PHE A 269 TYR 0.012 0.002 TYR A 275 ARG 0.001 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 308) hydrogen bonds : angle 4.47883 ( 888) SS BOND : bond 0.00439 ( 2) SS BOND : angle 2.99944 ( 4) covalent geometry : bond 0.00283 ( 4099) covalent geometry : angle 0.63387 ( 5601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7456 (tp40) REVERT: A 284 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6138 (ttm-80) REVERT: A 324 MET cc_start: 0.6918 (mmm) cc_final: 0.6699 (mmm) REVERT: A 356 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8356 (t) REVERT: A 394 MET cc_start: 0.5734 (mmt) cc_final: 0.5444 (mmp) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1643 time to fit residues: 17.2478 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.0040 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4624 r_free = 0.4624 target = 0.246452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.200211 restraints weight = 4871.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.206380 restraints weight = 2784.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.210524 restraints weight = 1882.371| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4101 Z= 0.147 Angle : 0.638 10.634 5605 Z= 0.310 Chirality : 0.038 0.118 661 Planarity : 0.005 0.051 697 Dihedral : 4.211 15.626 561 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.11 % Allowed : 23.67 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.37), residues: 526 helix: 1.87 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.10 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 120 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 358 TYR 0.018 0.002 TYR A 180 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 308) hydrogen bonds : angle 4.44897 ( 888) SS BOND : bond 0.00209 ( 2) SS BOND : angle 2.07465 ( 4) covalent geometry : bond 0.00298 ( 4099) covalent geometry : angle 0.63541 ( 5601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5294 (ttt180) cc_final: 0.4871 (ttt90) REVERT: A 95 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7406 (tp40) REVERT: A 120 TRP cc_start: 0.8109 (m100) cc_final: 0.7775 (m100) REVERT: A 147 MET cc_start: 0.6401 (mtt) cc_final: 0.6056 (tpp) REVERT: A 284 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6276 (ttm-80) REVERT: A 324 MET cc_start: 0.7013 (mmm) cc_final: 0.6659 (mmm) REVERT: A 356 CYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8346 (t) REVERT: A 394 MET cc_start: 0.5688 (mmt) cc_final: 0.5298 (mmm) REVERT: A 466 MET cc_start: 0.6252 (mmp) cc_final: 0.5894 (mmp) outliers start: 17 outliers final: 14 residues processed: 81 average time/residue: 0.2311 time to fit residues: 23.6542 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.243745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.197278 restraints weight = 4914.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.203321 restraints weight = 2830.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.207129 restraints weight = 1930.565| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4101 Z= 0.151 Angle : 0.637 10.115 5605 Z= 0.312 Chirality : 0.038 0.120 661 Planarity : 0.005 0.053 697 Dihedral : 4.175 15.212 561 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.31 % Allowed : 23.67 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.38), residues: 526 helix: 1.92 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.21 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 120 HIS 0.002 0.000 HIS A 47 PHE 0.012 0.001 PHE A 358 TYR 0.015 0.002 TYR A 180 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 308) hydrogen bonds : angle 4.49233 ( 888) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.84737 ( 4) covalent geometry : bond 0.00311 ( 4099) covalent geometry : angle 0.63548 ( 5601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5747 (ttt180) cc_final: 0.5014 (ttm170) REVERT: A 95 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7389 (tp40) REVERT: A 120 TRP cc_start: 0.8183 (m100) cc_final: 0.7888 (m100) REVERT: A 147 MET cc_start: 0.6465 (mtt) cc_final: 0.6169 (tpp) REVERT: A 284 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6275 (ttm-80) REVERT: A 324 MET cc_start: 0.6980 (mmm) cc_final: 0.6644 (mmm) REVERT: A 356 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8425 (t) REVERT: A 394 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5414 (mmm) REVERT: A 453 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6492 (m) REVERT: A 466 MET cc_start: 0.6274 (mmp) cc_final: 0.6064 (mmp) outliers start: 22 outliers final: 15 residues processed: 81 average time/residue: 0.2094 time to fit residues: 23.4605 Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.242600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195603 restraints weight = 4802.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201748 restraints weight = 2762.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.205818 restraints weight = 1884.534| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4101 Z= 0.149 Angle : 0.638 9.299 5605 Z= 0.313 Chirality : 0.038 0.118 661 Planarity : 0.005 0.054 697 Dihedral : 4.151 15.068 561 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.31 % Allowed : 24.15 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.37), residues: 526 helix: 1.94 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.23 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.001 0.000 HIS A 47 PHE 0.030 0.002 PHE A 348 TYR 0.014 0.002 TYR A 180 ARG 0.002 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05611 ( 308) hydrogen bonds : angle 4.43024 ( 888) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.76744 ( 4) covalent geometry : bond 0.00308 ( 4099) covalent geometry : angle 0.63637 ( 5601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5504 (ttt180) cc_final: 0.4997 (ttm170) REVERT: A 95 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7402 (tp40) REVERT: A 120 TRP cc_start: 0.8208 (m100) cc_final: 0.7925 (m100) REVERT: A 147 MET cc_start: 0.6520 (mtt) cc_final: 0.6297 (tpp) REVERT: A 284 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6233 (ttm-80) REVERT: A 324 MET cc_start: 0.7053 (mmm) cc_final: 0.6732 (mmm) REVERT: A 356 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 394 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5459 (mmm) REVERT: A 453 THR cc_start: 0.7065 (OUTLIER) cc_final: 0.5506 (p) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.1434 time to fit residues: 16.0265 Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4620 r_free = 0.4620 target = 0.245836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199245 restraints weight = 4861.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.205627 restraints weight = 2767.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.209904 restraints weight = 1866.422| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4101 Z= 0.140 Angle : 0.648 9.681 5605 Z= 0.313 Chirality : 0.038 0.120 661 Planarity : 0.005 0.051 697 Dihedral : 4.122 14.778 561 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.35 % Allowed : 25.85 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.38), residues: 526 helix: 2.01 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.32 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.001 0.000 HIS A 47 PHE 0.039 0.002 PHE A 348 TYR 0.013 0.002 TYR A 275 ARG 0.001 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.05383 ( 308) hydrogen bonds : angle 4.32949 ( 888) SS BOND : bond 0.00241 ( 2) SS BOND : angle 1.66008 ( 4) covalent geometry : bond 0.00273 ( 4099) covalent geometry : angle 0.64677 ( 5601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.5896 (tt) cc_final: 0.5561 (tt) REVERT: A 90 ARG cc_start: 0.5697 (ttt180) cc_final: 0.5236 (ttm170) REVERT: A 95 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7476 (tp40) REVERT: A 120 TRP cc_start: 0.8097 (m100) cc_final: 0.7855 (m100) REVERT: A 147 MET cc_start: 0.6488 (mtt) cc_final: 0.6269 (tpp) REVERT: A 284 ARG cc_start: 0.6868 (ttm-80) cc_final: 0.6064 (ttm-80) REVERT: A 324 MET cc_start: 0.7034 (mmm) cc_final: 0.6712 (mmm) REVERT: A 356 CYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8481 (t) REVERT: A 394 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5433 (mmm) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.1294 time to fit residues: 14.0700 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 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 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.243716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196707 restraints weight = 4890.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.203050 restraints weight = 2799.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207288 restraints weight = 1898.095| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4101 Z= 0.149 Angle : 0.675 10.215 5605 Z= 0.328 Chirality : 0.039 0.127 661 Planarity : 0.005 0.052 697 Dihedral : 4.107 14.497 561 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.86 % Allowed : 25.60 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.37), residues: 526 helix: 1.89 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.39 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.000 HIS A 47 PHE 0.039 0.002 PHE A 348 TYR 0.016 0.002 TYR A 275 ARG 0.001 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 308) hydrogen bonds : angle 4.42717 ( 888) SS BOND : bond 0.00223 ( 2) SS BOND : angle 1.58885 ( 4) covalent geometry : bond 0.00304 ( 4099) covalent geometry : angle 0.67392 ( 5601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: A 90 ARG cc_start: 0.5898 (ttt180) cc_final: 0.5284 (ttm170) REVERT: A 95 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7442 (tp40) REVERT: A 120 TRP cc_start: 0.8109 (m100) cc_final: 0.7868 (m100) REVERT: A 147 MET cc_start: 0.6502 (mtt) cc_final: 0.6285 (tpp) REVERT: A 284 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6088 (ttm-80) REVERT: A 324 MET cc_start: 0.7064 (mmm) cc_final: 0.6747 (mmm) REVERT: A 356 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (t) REVERT: A 394 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5444 (mmm) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1430 time to fit residues: 14.0885 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.244002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.197335 restraints weight = 4886.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.203664 restraints weight = 2829.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.207986 restraints weight = 1911.486| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4101 Z= 0.153 Angle : 0.678 9.862 5605 Z= 0.331 Chirality : 0.039 0.127 661 Planarity : 0.005 0.051 697 Dihedral : 4.131 14.486 561 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.86 % Allowed : 25.36 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.37), residues: 526 helix: 1.90 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.38 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.000 HIS A 47 PHE 0.039 0.002 PHE A 348 TYR 0.016 0.002 TYR A 275 ARG 0.002 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.05464 ( 308) hydrogen bonds : angle 4.43148 ( 888) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.57443 ( 4) covalent geometry : bond 0.00315 ( 4099) covalent geometry : angle 0.67739 ( 5601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.48 seconds wall clock time: 43 minutes 45.02 seconds (2625.02 seconds total)