Starting phenix.real_space_refine on Thu Sep 10 20:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.cif" model { file = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m49_30074/09_2026/6m49_30074.cif" } resolution = 3.7 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= 0.007 sd= 0.106 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 17 5.16 5 C 2049 2.51 5 N 495 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1382 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1687 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'HC3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.88, per 1000 atoms: 0.28 Number of scatterers: 3098 At special positions: 0 Unit cell: (85.873, 78.264, 75.003, 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 17 16.00 O 537 8.00 N 495 7.00 C 2049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.28 Conformation dependent library (CDL) restraints added in 102.1 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 51 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 72 through 96 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 130 through 149 Processing helix chain 'A' and resid 153 through 173 removed outlier: 3.607A pdb=" N LEU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 190 through 214 removed outlier: 4.262A pdb=" N CYS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 4.025A pdb=" N TYR B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 47 Proline residue: B 43 - end of helix removed outlier: 3.765A pdb=" N LYS B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 305 Processing helix chain 'B' and resid 313 through 338 removed outlier: 4.050A pdb=" N LEU B 317 " --> pdb=" O TRP B 313 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.663A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 388 through 408 Processing helix chain 'B' and resid 411 through 449 removed outlier: 4.347A pdb=" N THR B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 556 269 hydrogen bonds defined for protein. 804 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: 0.35 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 944 1.34 - 1.46: 744 1.46 - 1.58: 1450 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3163 Sorted by residual: bond pdb=" N VAL B 309 " pdb=" CA VAL B 309 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.09e+00 bond pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.81e+00 bond pdb=" N GLU B 376 " pdb=" CA GLU B 376 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.27e-02 6.20e+03 7.79e+00 bond pdb=" N GLN A 50 " pdb=" CA GLN A 50 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.32e+00 bond pdb=" N VAL B 377 " pdb=" CA VAL B 377 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.97e+00 ... (remaining 3158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4067 1.56 - 3.13: 201 3.13 - 4.69: 46 4.69 - 6.25: 9 6.25 - 7.82: 2 Bond angle restraints: 4325 Sorted by residual: angle pdb=" CA VAL B 309 " pdb=" C VAL B 309 " pdb=" O VAL B 309 " ideal model delta sigma weight residual 121.58 117.64 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ASP B 374 " pdb=" C ASP B 374 " pdb=" O ASP B 374 " ideal model delta sigma weight residual 120.66 116.41 4.25 1.15e+00 7.56e-01 1.36e+01 angle pdb=" C ASP B 307 " pdb=" N MET B 308 " pdb=" CA MET B 308 " ideal model delta sigma weight residual 122.21 127.93 -5.72 1.62e+00 3.81e-01 1.25e+01 angle pdb=" C VAL B 309 " pdb=" N LYS B 310 " pdb=" CA LYS B 310 " ideal model delta sigma weight residual 122.40 127.49 -5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" N VAL B 373 " pdb=" CA VAL B 373 " pdb=" C VAL B 373 " ideal model delta sigma weight residual 111.77 108.19 3.58 1.04e+00 9.25e-01 1.19e+01 ... (remaining 4320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1569 14.05 - 28.10: 161 28.10 - 42.15: 69 42.15 - 56.19: 12 56.19 - 70.24: 3 Dihedral angle restraints: 1814 sinusoidal: 611 harmonic: 1203 Sorted by residual: dihedral pdb=" CA LEU B 285 " pdb=" C LEU B 285 " pdb=" N ILE B 286 " pdb=" CA ILE B 286 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP A 72 " pdb=" C TRP A 72 " pdb=" N VAL A 73 " pdb=" CA VAL A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 212 " pdb=" C MET A 212 " pdb=" N TYR A 213 " pdb=" CA TYR A 213 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 401 0.049 - 0.098: 114 0.098 - 0.147: 19 0.147 - 0.195: 4 0.195 - 0.244: 2 Chirality restraints: 540 Sorted by residual: chirality pdb=" C10 HC3 A 501 " pdb=" C1 HC3 A 501 " pdb=" C5 HC3 A 501 " pdb=" C9 HC3 A 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA VAL B 377 " pdb=" N VAL B 377 " pdb=" C VAL B 377 " pdb=" CB VAL B 377 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 104 " pdb=" N GLU A 104 " pdb=" C GLU A 104 " pdb=" CB GLU A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 537 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 373 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C VAL B 373 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 373 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 374 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 433 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C MET B 433 " -0.044 2.00e-02 2.50e+03 pdb=" O MET B 433 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 434 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 11 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C ILE B 11 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B 11 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 12 " -0.011 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 61 2.64 - 3.21: 3474 3.21 - 3.77: 4776 3.77 - 4.34: 5906 4.34 - 4.90: 9329 Nonbonded interactions: 23546 Sorted by model distance: nonbonded pdb=" O GLN A 52 " pdb=" NE2 GLN A 52 " model vdw 2.079 3.120 nonbonded pdb=" O ARG A 53 " pdb=" OD1 ASN A 54 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 406 " pdb=" OG1 THR B 409 " model vdw 2.266 3.040 nonbonded pdb=" O PHE A 163 " pdb=" OG1 THR A 166 " model vdw 2.298 3.040 nonbonded pdb=" O PRO B 287 " pdb=" OG1 THR B 291 " model vdw 2.299 3.040 ... (remaining 23541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.720 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.008 0.056 3163 Z= 0.398 Angle : 0.851 7.815 4325 Z= 0.500 Chirality : 0.048 0.244 540 Planarity : 0.005 0.034 522 Dihedral : 14.317 70.242 1036 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.65 % Rotamer: Outliers : 0.98 % Allowed : 6.89 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.35), residues: 408 helix: -2.04 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -4.52 (0.55), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.015 0.002 TYR B 298 PHE 0.023 0.002 PHE B 429 TRP 0.018 0.002 TRP B 313 HIS 0.008 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.40 ( 3163) covalent geometry : angle 0.85080 / 0.50 ( 4325) hydrogen bonds : bond 0.12557 / 8.60 ( 269) hydrogen bonds : angle 6.50229 / 4.76 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.067 Fit side-chains REVERT: A 29 MET cc_start: 0.8511 (ttm) cc_final: 0.8305 (tmm) REVERT: A 102 LYS cc_start: 0.7823 (mttt) cc_final: 0.7198 (mtmt) REVERT: A 119 ASN cc_start: 0.8384 (t0) cc_final: 0.8107 (t0) REVERT: A 172 LEU cc_start: 0.8320 (pp) cc_final: 0.8078 (pp) REVERT: A 214 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7619 (tm-30) REVERT: B 344 ASN cc_start: 0.7140 (p0) cc_final: 0.6653 (p0) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.0506 time to fit residues: 7.7615 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.196319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.164564 restraints weight = 5240.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.168506 restraints weight = 3852.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.171232 restraints weight = 2180.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.171815 restraints weight = 1695.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.172854 restraints weight = 1572.133| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3163 Z= 0.154 Angle : 0.714 7.656 4325 Z= 0.352 Chirality : 0.039 0.108 540 Planarity : 0.004 0.029 522 Dihedral : 5.177 53.095 445 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.28 % Allowed : 18.03 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.40), residues: 408 helix: 0.71 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -3.70 (0.63), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.011 0.001 TYR B 16 PHE 0.013 0.001 PHE A 148 TRP 0.017 0.001 TRP A 191 HIS 0.006 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3163) covalent geometry : angle 0.71378 / 0.35 ( 4325) hydrogen bonds : bond 0.04344 / 2.84 ( 269) hydrogen bonds : angle 3.99516 / 2.91 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8382 (mttt) cc_final: 0.7878 (ttmt) REVERT: B 329 MET cc_start: 0.8180 (ttm) cc_final: 0.7929 (ttm) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 0.0473 time to fit residues: 6.4228 Evaluate side-chains 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 36 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.154113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122550 restraints weight = 6285.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.126320 restraints weight = 3332.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.127741 restraints weight = 2250.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127725 restraints weight = 1775.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128196 restraints weight = 1848.470| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3163 Z= 0.137 Angle : 0.708 9.594 4325 Z= 0.339 Chirality : 0.039 0.114 540 Planarity : 0.004 0.030 522 Dihedral : 4.919 52.999 445 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.28 % Allowed : 25.25 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.42), residues: 408 helix: 1.93 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -3.39 (0.63), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.012 0.001 TYR B 16 PHE 0.011 0.001 PHE A 148 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.003 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 3163) covalent geometry : angle 0.70764 / 0.34 ( 4325) hydrogen bonds : bond 0.04006 / 2.60 ( 269) hydrogen bonds : angle 3.63079 / 2.63 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.069 Fit side-chains REVERT: A 41 PHE cc_start: 0.8491 (t80) cc_final: 0.8217 (t80) REVERT: A 47 ASN cc_start: 0.8354 (t0) cc_final: 0.8135 (t0) REVERT: A 102 LYS cc_start: 0.7970 (mttt) cc_final: 0.7337 (ttmt) REVERT: B 296 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 298 TYR cc_start: 0.8474 (t80) cc_final: 0.6443 (t80) REVERT: B 329 MET cc_start: 0.8358 (ttm) cc_final: 0.7989 (ttm) REVERT: B 383 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 396 MET cc_start: 0.7209 (mmm) cc_final: 0.6901 (mtt) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.0517 time to fit residues: 7.0272 Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.148772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116045 restraints weight = 6265.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120701 restraints weight = 3458.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.121746 restraints weight = 2131.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121551 restraints weight = 1813.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121906 restraints weight = 1892.547| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3163 Z= 0.175 Angle : 0.740 12.535 4325 Z= 0.363 Chirality : 0.041 0.119 540 Planarity : 0.004 0.034 522 Dihedral : 5.005 56.303 445 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 8.85 % Allowed : 24.26 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.42), residues: 408 helix: 1.95 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -3.08 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.016 0.002 TYR B 351 PHE 0.009 0.001 PHE B 417 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 3163) covalent geometry : angle 0.74050 / 0.36 ( 4325) hydrogen bonds : bond 0.04475 / 2.87 ( 269) hydrogen bonds : angle 3.74020 / 2.74 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8435 (ptp) cc_final: 0.7925 (ppp) REVERT: A 47 ASN cc_start: 0.8468 (t0) cc_final: 0.8171 (t0) REVERT: A 50 GLN cc_start: 0.7147 (pt0) cc_final: 0.6894 (pt0) REVERT: A 102 LYS cc_start: 0.8259 (mttt) cc_final: 0.7797 (ttmt) REVERT: B 296 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7632 (t80) REVERT: B 298 TYR cc_start: 0.8633 (t80) cc_final: 0.7946 (t80) REVERT: B 329 MET cc_start: 0.8477 (ttm) cc_final: 0.8097 (ttm) REVERT: B 396 MET cc_start: 0.7385 (mmm) cc_final: 0.6993 (mtt) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 0.0478 time to fit residues: 7.2178 Evaluate side-chains 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 170 GLN B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.151184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117499 restraints weight = 6245.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119164 restraints weight = 3373.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121225 restraints weight = 2576.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.121243 restraints weight = 1926.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121872 restraints weight = 1966.350| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3163 Z= 0.137 Angle : 0.731 13.101 4325 Z= 0.348 Chirality : 0.039 0.126 540 Planarity : 0.004 0.057 522 Dihedral : 4.903 56.409 445 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.23 % Allowed : 30.16 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.42), residues: 408 helix: 2.09 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -3.11 (0.60), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 380 TYR 0.016 0.001 TYR B 351 PHE 0.013 0.001 PHE A 148 TRP 0.010 0.001 TRP A 191 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 3163) covalent geometry : angle 0.73064 / 0.35 ( 4325) hydrogen bonds : bond 0.03951 / 2.53 ( 269) hydrogen bonds : angle 3.54597 / 2.56 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8420 (ptp) cc_final: 0.7865 (ppp) REVERT: A 47 ASN cc_start: 0.8449 (t0) cc_final: 0.8163 (t0) REVERT: A 50 GLN cc_start: 0.7136 (pt0) cc_final: 0.6912 (pt0) REVERT: A 102 LYS cc_start: 0.8117 (mttt) cc_final: 0.7668 (ttpt) REVERT: B 15 PHE cc_start: 0.8927 (m-80) cc_final: 0.8726 (m-10) REVERT: B 286 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 296 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7679 (t80) REVERT: B 298 TYR cc_start: 0.8612 (t80) cc_final: 0.7743 (t80) REVERT: B 329 MET cc_start: 0.8413 (ttm) cc_final: 0.8038 (ttm) REVERT: B 347 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 396 MET cc_start: 0.7364 (mmm) cc_final: 0.6892 (mtt) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.0444 time to fit residues: 6.2870 Evaluate side-chains 112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 170 GLN B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.152395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.118574 restraints weight = 6194.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121042 restraints weight = 3421.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.122673 restraints weight = 2460.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.122914 restraints weight = 1909.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123310 restraints weight = 1961.071| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3163 Z= 0.133 Angle : 0.745 14.139 4325 Z= 0.348 Chirality : 0.041 0.231 540 Planarity : 0.004 0.056 522 Dihedral : 4.868 57.557 445 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.92 % Allowed : 32.13 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.42), residues: 408 helix: 2.16 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -2.98 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.012 0.001 TYR B 351 PHE 0.011 0.001 PHE A 148 TRP 0.010 0.001 TRP A 191 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3163) covalent geometry : angle 0.74500 / 0.35 ( 4325) hydrogen bonds : bond 0.03858 / 2.48 ( 269) hydrogen bonds : angle 3.51687 / 2.55 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8409 (ptp) cc_final: 0.7843 (ppp) REVERT: A 47 ASN cc_start: 0.8418 (t0) cc_final: 0.8119 (t0) REVERT: A 50 GLN cc_start: 0.7182 (pt0) cc_final: 0.6971 (pt0) REVERT: A 92 ASP cc_start: 0.9069 (m-30) cc_final: 0.8818 (m-30) REVERT: A 100 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8258 (mtmm) REVERT: A 102 LYS cc_start: 0.8124 (mttt) cc_final: 0.7442 (ttmt) REVERT: B 286 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 298 TYR cc_start: 0.8625 (t80) cc_final: 0.6352 (t80) REVERT: B 329 MET cc_start: 0.8339 (ttm) cc_final: 0.7931 (ttm) REVERT: B 396 MET cc_start: 0.7407 (mmm) cc_final: 0.6981 (mtt) REVERT: B 400 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7395 (tt) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.0497 time to fit residues: 7.0247 Evaluate side-chains 110 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.153969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.121126 restraints weight = 6262.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121646 restraints weight = 3439.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.124319 restraints weight = 2737.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124306 restraints weight = 1970.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.125091 restraints weight = 2000.633| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3163 Z= 0.134 Angle : 0.739 13.499 4325 Z= 0.349 Chirality : 0.040 0.171 540 Planarity : 0.004 0.056 522 Dihedral : 4.826 58.641 445 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.59 % Allowed : 36.07 % Favored : 59.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.41), residues: 408 helix: 2.19 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -3.00 (0.60), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.013 0.001 TYR B 351 PHE 0.015 0.001 PHE A 127 TRP 0.010 0.001 TRP A 191 HIS 0.005 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3163) covalent geometry : angle 0.73941 / 0.35 ( 4325) hydrogen bonds : bond 0.03748 / 2.42 ( 269) hydrogen bonds : angle 3.42408 / 2.47 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8440 (ptp) cc_final: 0.7812 (ppp) REVERT: A 47 ASN cc_start: 0.8378 (t0) cc_final: 0.8082 (t0) REVERT: A 50 GLN cc_start: 0.6987 (pt0) cc_final: 0.6771 (pt0) REVERT: A 100 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8373 (mtmt) REVERT: A 102 LYS cc_start: 0.7918 (mttt) cc_final: 0.7543 (ttpt) REVERT: A 155 PHE cc_start: 0.8502 (t80) cc_final: 0.8216 (t80) REVERT: B 286 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8080 (tt) REVERT: B 329 MET cc_start: 0.8362 (ttm) cc_final: 0.8108 (ttm) REVERT: B 365 THR cc_start: 0.8360 (p) cc_final: 0.8157 (t) REVERT: B 396 MET cc_start: 0.7426 (mmm) cc_final: 0.6964 (mtt) REVERT: B 400 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7465 (tt) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.0540 time to fit residues: 7.2863 Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.152196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.118196 restraints weight = 6367.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.120788 restraints weight = 3491.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122932 restraints weight = 2486.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.122601 restraints weight = 1912.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123159 restraints weight = 2013.795| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3163 Z= 0.141 Angle : 0.762 12.308 4325 Z= 0.366 Chirality : 0.045 0.394 540 Planarity : 0.005 0.056 522 Dihedral : 4.812 59.542 445 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.25 % Allowed : 34.75 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.42), residues: 408 helix: 2.33 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.98 (0.61), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 150 TYR 0.022 0.001 TYR B 351 PHE 0.014 0.001 PHE A 127 TRP 0.011 0.001 TRP A 191 HIS 0.005 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 3163) covalent geometry : angle 0.76250 / 0.37 ( 4325) hydrogen bonds : bond 0.03869 / 2.45 ( 269) hydrogen bonds : angle 3.46557 / 2.53 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8404 (ptp) cc_final: 0.7749 (ppp) REVERT: A 47 ASN cc_start: 0.8387 (t0) cc_final: 0.8127 (t0) REVERT: A 50 GLN cc_start: 0.7027 (pt0) cc_final: 0.6795 (pt0) REVERT: A 75 PRO cc_start: 0.7878 (Cg_exo) cc_final: 0.7645 (Cg_endo) REVERT: A 100 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8423 (mtmt) REVERT: A 102 LYS cc_start: 0.7920 (mttt) cc_final: 0.7506 (ttpt) REVERT: B 286 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 298 TYR cc_start: 0.8633 (t80) cc_final: 0.6458 (t80) REVERT: B 329 MET cc_start: 0.8399 (ttm) cc_final: 0.7938 (ttm) REVERT: B 333 LEU cc_start: 0.9051 (tt) cc_final: 0.8842 (mm) REVERT: B 396 MET cc_start: 0.7393 (mmm) cc_final: 0.6888 (mtt) REVERT: B 400 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7456 (tt) REVERT: B 429 PHE cc_start: 0.7872 (t80) cc_final: 0.7631 (t80) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.0491 time to fit residues: 7.1628 Evaluate side-chains 109 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.115746 restraints weight = 6386.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.119158 restraints weight = 3527.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.120601 restraints weight = 2374.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.120324 restraints weight = 1913.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120788 restraints weight = 2010.426| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3163 Z= 0.158 Angle : 0.798 14.550 4325 Z= 0.382 Chirality : 0.045 0.395 540 Planarity : 0.005 0.056 522 Dihedral : 4.855 58.667 445 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 7.21 % Allowed : 33.44 % Favored : 59.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.42), residues: 408 helix: 2.20 (0.27), residues: 340 sheet: None (None), residues: 0 loop : -2.84 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.010 0.001 TYR B 16 PHE 0.014 0.001 PHE A 127 TRP 0.010 0.001 TRP A 191 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 3163) covalent geometry : angle 0.79809 / 0.38 ( 4325) hydrogen bonds : bond 0.04162 / 2.61 ( 269) hydrogen bonds : angle 3.60506 / 2.64 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8405 (ptp) cc_final: 0.7731 (ppp) REVERT: A 47 ASN cc_start: 0.8452 (t0) cc_final: 0.8204 (t0) REVERT: A 75 PRO cc_start: 0.7874 (Cg_exo) cc_final: 0.7627 (Cg_endo) REVERT: A 100 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8300 (mtmm) REVERT: A 102 LYS cc_start: 0.8160 (mttt) cc_final: 0.7427 (ttmt) REVERT: A 144 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 286 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8158 (tt) REVERT: B 296 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7682 (t80) REVERT: B 298 TYR cc_start: 0.8717 (t80) cc_final: 0.6775 (t80) REVERT: B 396 MET cc_start: 0.7622 (mmm) cc_final: 0.7016 (mtt) REVERT: B 429 PHE cc_start: 0.7955 (t80) cc_final: 0.7650 (t80) outliers start: 22 outliers final: 15 residues processed: 110 average time/residue: 0.0517 time to fit residues: 7.2135 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.151234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.117616 restraints weight = 6224.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119340 restraints weight = 3390.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.121114 restraints weight = 2545.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121295 restraints weight = 1965.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121757 restraints weight = 2037.116| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3163 Z= 0.149 Angle : 0.809 13.851 4325 Z= 0.386 Chirality : 0.045 0.389 540 Planarity : 0.005 0.055 522 Dihedral : 4.832 57.455 445 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.90 % Allowed : 35.41 % Favored : 58.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.42), residues: 408 helix: 2.24 (0.27), residues: 340 sheet: None (None), residues: 0 loop : -2.88 (0.64), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.009 0.001 TYR B 16 PHE 0.014 0.001 PHE A 127 TRP 0.012 0.001 TRP A 105 HIS 0.006 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 3163) covalent geometry : angle 0.80885 / 0.39 ( 4325) hydrogen bonds : bond 0.03992 / 2.52 ( 269) hydrogen bonds : angle 3.57279 / 2.61 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8442 (ptp) cc_final: 0.7781 (ppp) REVERT: A 47 ASN cc_start: 0.8301 (t0) cc_final: 0.7986 (t0) REVERT: A 75 PRO cc_start: 0.7775 (Cg_exo) cc_final: 0.7533 (Cg_endo) REVERT: A 102 LYS cc_start: 0.8103 (mttt) cc_final: 0.7478 (ttmt) REVERT: B 286 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8122 (tt) REVERT: B 296 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 298 TYR cc_start: 0.8667 (t80) cc_final: 0.6631 (t80) REVERT: B 396 MET cc_start: 0.7499 (mmm) cc_final: 0.6919 (mtt) outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.0494 time to fit residues: 6.7687 Evaluate side-chains 110 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 0.0270 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.120238 restraints weight = 6219.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121609 restraints weight = 3515.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.124065 restraints weight = 2647.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.123863 restraints weight = 1966.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124630 restraints weight = 2010.002| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3163 Z= 0.143 Angle : 0.813 13.817 4325 Z= 0.381 Chirality : 0.044 0.386 540 Planarity : 0.005 0.054 522 Dihedral : 4.770 56.176 445 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.25 % Allowed : 36.39 % Favored : 58.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.42), residues: 408 helix: 2.22 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -2.77 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 189 TYR 0.010 0.001 TYR B 16 PHE 0.018 0.001 PHE A 41 TRP 0.011 0.001 TRP A 105 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3163) covalent geometry : angle 0.81308 / 0.38 ( 4325) hydrogen bonds : bond 0.03782 / 2.39 ( 269) hydrogen bonds : angle 3.51527 / 2.57 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 726.26 seconds wall clock time: 13 minutes 9.55 seconds (789.55 seconds total)