Starting phenix.real_space_refine on Fri Aug 22 14:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjq_37589/08_2025/8wjq_37589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjq_37589/08_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_37589/08_2025/8wjq_37589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjq_37589/08_2025/8wjq_37589.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjq_37589/08_2025/8wjq_37589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjq_37589/08_2025/8wjq_37589.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG: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: 1.18, per 1000 atoms: 0.30 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: 0.36 Conformation dependent library (CDL) restraints added in 148.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.61 Time building geometry restraints manager: 0.46 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: 0.420 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.830 Find NCS groups from input model: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.044 0.004 ARG A 92 TYR 0.027 0.006 TYR A 275 PHE 0.036 0.004 PHE A 348 TRP 0.102 0.004 TRP A 135 HIS 0.016 0.003 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00983 ( 4099) covalent geometry : angle 1.47004 ( 5601) SS BOND : bond 0.00812 ( 2) SS BOND : angle 2.30303 ( 4) hydrogen bonds : bond 0.12570 ( 308) hydrogen bonds : angle 5.82813 ( 888) *********************** 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 : 0.147 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: 0.0634 time to fit residues: 6.1372 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.0970 chunk 50 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.1974 ------------------------------------------------------------------------------- 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 = 0.4783 r_free = 0.4783 target = 0.268410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.225902 restraints weight = 4846.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.232868 restraints weight = 2642.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.237666 restraints weight = 1702.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.240295 restraints weight = 1259.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.242544 restraints weight = 1039.177| |-----------------------------------------------------------------------------| r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.1217 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= 0.160 Angle : 0.700 10.122 5605 Z= 0.356 Chirality : 0.041 0.174 661 Planarity : 0.008 0.091 697 Dihedral : 4.340 16.663 561 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.14 % Allowed : 16.43 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.37), residues: 526 helix: 1.53 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.40 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 92 TYR 0.021 0.002 TYR A 275 PHE 0.015 0.002 PHE A 269 TRP 0.029 0.002 TRP A 135 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4099) covalent geometry : angle 0.69936 ( 5601) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.64755 ( 4) hydrogen bonds : bond 0.05915 ( 308) hydrogen bonds : angle 4.71528 ( 888) *********************** 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 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.088 Fit side-chains REVERT: A 120 TRP cc_start: 0.7111 (m-90) cc_final: 0.6471 (m-90) REVERT: A 177 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7173 (m) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 0.0512 time to fit residues: 5.5921 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4725 r_free = 0.4725 target = 0.259354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.214992 restraints weight = 4852.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.221111 restraints weight = 2766.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.225377 restraints weight = 1849.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.227727 restraints weight = 1413.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.229936 restraints weight = 1195.446| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4101 Z= 0.164 Angle : 0.688 11.121 5605 Z= 0.341 Chirality : 0.041 0.245 661 Planarity : 0.006 0.063 697 Dihedral : 4.220 14.241 561 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.14 % Allowed : 18.84 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 526 helix: 1.73 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.52 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.017 0.002 TYR A 275 PHE 0.028 0.002 PHE A 348 TRP 0.015 0.002 TRP A 135 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4099) covalent geometry : angle 0.68650 ( 5601) SS BOND : bond 0.00657 ( 2) SS BOND : angle 1.70367 ( 4) hydrogen bonds : bond 0.05915 ( 308) hydrogen bonds : angle 4.58479 ( 888) *********************** 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 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5784 (tp) cc_final: 0.4823 (tt) REVERT: A 95 GLN cc_start: 0.7480 (tp-100) cc_final: 0.7040 (tp-100) REVERT: A 135 TRP cc_start: 0.7424 (m-10) cc_final: 0.6305 (m-10) REVERT: A 177 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7085 (m) REVERT: A 324 MET cc_start: 0.6650 (mmm) cc_final: 0.6206 (mmm) REVERT: A 428 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.5415 (t-90) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.0619 time to fit residues: 6.6291 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 428 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 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.272121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.226642 restraints weight = 4769.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.233432 restraints weight = 2643.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.238046 restraints weight = 1737.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.240697 restraints weight = 1307.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.242919 restraints weight = 1101.475| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.2204 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= 0.151 Angle : 0.652 11.044 5605 Z= 0.319 Chirality : 0.039 0.169 661 Planarity : 0.005 0.057 697 Dihedral : 4.175 14.016 561 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.14 % Allowed : 21.74 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 526 helix: 1.75 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.62 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.015 0.002 TYR A 275 PHE 0.014 0.001 PHE A 358 TRP 0.013 0.001 TRP A 357 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4099) covalent geometry : angle 0.65087 ( 5601) SS BOND : bond 0.00571 ( 2) SS BOND : angle 1.46507 ( 4) hydrogen bonds : bond 0.05640 ( 308) hydrogen bonds : angle 4.47984 ( 888) *********************** 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 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.4649 (tt) REVERT: A 135 TRP cc_start: 0.7596 (m-10) cc_final: 0.6913 (m-10) REVERT: A 177 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7057 (m) REVERT: A 284 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6248 (ttm-80) REVERT: A 324 MET cc_start: 0.6672 (mmm) cc_final: 0.6456 (mmm) REVERT: A 471 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6965 (tt) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.0605 time to fit residues: 6.2546 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 LEU 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 Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.249874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.205291 restraints weight = 4863.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.211111 restraints weight = 2788.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.215187 restraints weight = 1893.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.217374 restraints weight = 1466.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.219389 restraints weight = 1254.807| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4101 Z= 0.161 Angle : 0.659 10.776 5605 Z= 0.324 Chirality : 0.040 0.161 661 Planarity : 0.005 0.060 697 Dihedral : 4.318 17.050 561 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.11 % Allowed : 22.46 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.37), residues: 526 helix: 1.77 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -0.80 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.015 0.002 TYR A 275 PHE 0.014 0.002 PHE A 358 TRP 0.029 0.002 TRP A 120 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4099) covalent geometry : angle 0.65450 ( 5601) SS BOND : bond 0.00330 ( 2) SS BOND : angle 2.83509 ( 4) hydrogen bonds : bond 0.05736 ( 308) hydrogen bonds : angle 4.55002 ( 888) *********************** 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 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.5348 (mmp) cc_final: 0.4764 (mmp) REVERT: A 37 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.4577 (tt) REVERT: A 90 ARG cc_start: 0.5892 (ttt180) cc_final: 0.5541 (ttt90) REVERT: A 95 GLN cc_start: 0.7481 (tp-100) cc_final: 0.6984 (tp-100) REVERT: A 120 TRP cc_start: 0.8004 (m100) cc_final: 0.7756 (m100) REVERT: A 284 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6309 (ttm-80) REVERT: A 324 MET cc_start: 0.6602 (mmm) cc_final: 0.6361 (mmm) REVERT: A 356 CYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 471 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7048 (tt) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.0577 time to fit residues: 6.2077 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 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 471 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.4809 r_free = 0.4809 target = 0.273396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.226986 restraints weight = 4860.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.234185 restraints weight = 2655.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.239090 restraints weight = 1711.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.242064 restraints weight = 1269.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.244249 restraints weight = 1045.240| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4101 Z= 0.143 Angle : 0.647 10.766 5605 Z= 0.310 Chirality : 0.039 0.147 661 Planarity : 0.005 0.056 697 Dihedral : 4.234 15.803 561 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.62 % Allowed : 23.19 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.38), residues: 526 helix: 1.91 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.06 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.013 0.002 TYR A 275 PHE 0.020 0.001 PHE A 348 TRP 0.015 0.001 TRP A 120 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4099) covalent geometry : angle 0.64409 ( 5601) SS BOND : bond 0.00356 ( 2) SS BOND : angle 2.20180 ( 4) hydrogen bonds : bond 0.05408 ( 308) hydrogen bonds : angle 4.41985 ( 888) *********************** 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 90 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.5260 (mmp) cc_final: 0.4785 (mmp) REVERT: A 37 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.4781 (tt) REVERT: A 95 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7059 (tp40) REVERT: A 120 TRP cc_start: 0.7966 (m100) cc_final: 0.7762 (m100) REVERT: A 284 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6180 (ttm-80) REVERT: A 324 MET cc_start: 0.6628 (mmm) cc_final: 0.6425 (mmm) REVERT: A 356 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8309 (t) REVERT: A 453 THR cc_start: 0.7179 (t) cc_final: 0.5461 (p) REVERT: A 471 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6941 (tt) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.0700 time to fit residues: 7.4659 Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 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 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4641 r_free = 0.4641 target = 0.249059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202382 restraints weight = 4976.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.208502 restraints weight = 2864.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.212730 restraints weight = 1938.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.215364 restraints weight = 1487.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.216619 restraints weight = 1261.306| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.3024 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= 0.154 Angle : 0.659 10.076 5605 Z= 0.320 Chirality : 0.039 0.116 661 Planarity : 0.005 0.052 697 Dihedral : 4.221 16.271 561 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.62 % Allowed : 24.88 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.38), residues: 526 helix: 1.92 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.16 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.020 0.002 TYR A 180 PHE 0.012 0.001 PHE A 273 TRP 0.012 0.001 TRP A 120 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4099) covalent geometry : angle 0.65678 ( 5601) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.89973 ( 4) hydrogen bonds : bond 0.05550 ( 308) hydrogen bonds : angle 4.51273 ( 888) *********************** 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 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.5518 (mmp) cc_final: 0.5180 (mmp) REVERT: A 37 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.4989 (tt) REVERT: A 90 ARG cc_start: 0.5572 (ttt180) cc_final: 0.5100 (ttt90) REVERT: A 95 GLN cc_start: 0.7458 (tp-100) cc_final: 0.7023 (tp40) REVERT: A 147 MET cc_start: 0.6429 (mtt) cc_final: 0.5985 (tpp) REVERT: A 234 MET cc_start: 0.7494 (mtm) cc_final: 0.7219 (mpp) REVERT: A 284 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6296 (ttm-80) REVERT: A 324 MET cc_start: 0.6660 (mmm) cc_final: 0.6270 (mmm) REVERT: A 356 CYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 471 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7077 (tt) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.0521 time to fit residues: 5.3672 Evaluate side-chains 75 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 LEU 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 245 HIS Chi-restraints excluded: chain A residue 277 TRP 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 471 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 = 0.4645 r_free = 0.4645 target = 0.249264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.202909 restraints weight = 4908.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.209161 restraints weight = 2824.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213340 restraints weight = 1912.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.215687 restraints weight = 1476.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.216702 restraints weight = 1255.606| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.3213 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 : 0.648 9.660 5605 Z= 0.314 Chirality : 0.039 0.116 661 Planarity : 0.005 0.052 697 Dihedral : 4.223 16.885 561 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.11 % Allowed : 23.91 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.38), residues: 526 helix: 1.95 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.14 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.015 0.002 TYR A 180 PHE 0.012 0.001 PHE A 358 TRP 0.017 0.001 TRP A 120 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4099) covalent geometry : angle 0.64596 ( 5601) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.87260 ( 4) hydrogen bonds : bond 0.05425 ( 308) hydrogen bonds : angle 4.46253 ( 888) *********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5164 (tt) REVERT: A 90 ARG cc_start: 0.5462 (ttt180) cc_final: 0.4719 (ttm170) REVERT: A 95 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7062 (tp40) REVERT: A 147 MET cc_start: 0.6395 (mtt) cc_final: 0.6006 (tpp) REVERT: A 284 ARG cc_start: 0.7015 (ttm-80) cc_final: 0.6177 (ttm-80) REVERT: A 324 MET cc_start: 0.6800 (mmm) cc_final: 0.6420 (mmm) REVERT: A 356 CYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 471 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7034 (tt) outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 0.0516 time to fit residues: 5.4248 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 157 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP 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 471 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.243155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201316 restraints weight = 4271.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.206529 restraints weight = 2510.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.210425 restraints weight = 1711.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212368 restraints weight = 1313.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.214576 restraints weight = 1121.730| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4101 Z= 0.177 Angle : 0.710 9.532 5605 Z= 0.349 Chirality : 0.041 0.141 661 Planarity : 0.005 0.060 697 Dihedral : 4.361 17.083 561 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 25.12 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.38), residues: 526 helix: 1.76 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.30 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.016 0.002 TYR A 275 PHE 0.030 0.002 PHE A 348 TRP 0.019 0.002 TRP A 135 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4099) covalent geometry : angle 0.70850 ( 5601) SS BOND : bond 0.00416 ( 2) SS BOND : angle 1.83268 ( 4) hydrogen bonds : bond 0.06026 ( 308) hydrogen bonds : angle 4.72833 ( 888) *********************** 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 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.5784 (tt) REVERT: A 90 ARG cc_start: 0.5719 (ttt180) cc_final: 0.4875 (ttm170) REVERT: A 120 TRP cc_start: 0.7851 (m100) cc_final: 0.7291 (m100) REVERT: A 147 MET cc_start: 0.6593 (mtt) cc_final: 0.6286 (tpp) REVERT: A 284 ARG cc_start: 0.7040 (ttm-80) cc_final: 0.6306 (ttm-80) REVERT: A 324 MET cc_start: 0.7141 (mmm) cc_final: 0.6868 (mmm) REVERT: A 356 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8462 (t) REVERT: A 471 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7220 (tt) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.0580 time to fit residues: 5.9421 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 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 419 CYS Chi-restraints excluded: chain A residue 471 LEU 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 11 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.0050 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.247487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.202164 restraints weight = 4919.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.208144 restraints weight = 2827.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.212409 restraints weight = 1934.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.215013 restraints weight = 1483.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.216335 restraints weight = 1254.877| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4101 Z= 0.147 Angle : 0.672 9.137 5605 Z= 0.326 Chirality : 0.040 0.161 661 Planarity : 0.005 0.056 697 Dihedral : 4.335 15.549 561 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.14 % Allowed : 26.57 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.38), residues: 526 helix: 1.92 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.25 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.016 0.002 TYR A 180 PHE 0.037 0.002 PHE A 348 TRP 0.013 0.002 TRP A 278 HIS 0.013 0.002 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4099) covalent geometry : angle 0.67097 ( 5601) SS BOND : bond 0.00355 ( 2) SS BOND : angle 1.76599 ( 4) hydrogen bonds : bond 0.05484 ( 308) hydrogen bonds : angle 4.46442 ( 888) ********************** 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 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5878 (tt) REVERT: A 90 ARG cc_start: 0.5746 (ttt180) cc_final: 0.5231 (ttm170) REVERT: A 147 MET cc_start: 0.6390 (mtt) cc_final: 0.6089 (tpp) REVERT: A 284 ARG cc_start: 0.7021 (ttm-80) cc_final: 0.6126 (ttm-80) REVERT: A 324 MET cc_start: 0.7051 (mmm) cc_final: 0.6702 (mmm) REVERT: A 356 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8376 (t) REVERT: A 471 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7092 (tt) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.0576 time to fit residues: 6.3832 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 471 LEU 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 32 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.246085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.202945 restraints weight = 4347.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208802 restraints weight = 2549.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.212533 restraints weight = 1726.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.215470 restraints weight = 1318.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.217232 restraints weight = 1102.173| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3941 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= 0.163 Angle : 0.689 8.409 5605 Z= 0.337 Chirality : 0.041 0.137 661 Planarity : 0.005 0.058 697 Dihedral : 4.338 16.098 561 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.38 % Allowed : 26.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.38), residues: 526 helix: 1.82 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.31 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.014 0.002 TYR A 275 PHE 0.037 0.002 PHE A 348 TRP 0.021 0.002 TRP A 135 HIS 0.013 0.002 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4099) covalent geometry : angle 0.68810 ( 5601) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.64122 ( 4) hydrogen bonds : bond 0.05684 ( 308) hydrogen bonds : angle 4.56659 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 917.57 seconds wall clock time: 16 minutes 29.39 seconds (989.39 seconds total)