Starting phenix.real_space_refine on Wed Mar 5 18:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m49_30074/03_2025/6m49_30074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m49_30074/03_2025/6m49_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_30074/03_2025/6m49_30074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2025/6m49_30074.map" model { file = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2025/6m49_30074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m49_30074/03_2025/6m49_30074.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'PHE:plan': 2, 'TYR:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: 2.76, per 1000 atoms: 0.89 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: 0.94 Conformation dependent library (CDL) restraints added in 397.2 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: 0.28 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: 0.87 Time building geometry restraints manager: 1.09 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: 1623 14.05 - 28.10: 161 28.10 - 42.15: 71 42.15 - 56.19: 12 56.19 - 70.24: 3 Dihedral angle restraints: 1870 sinusoidal: 667 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 1867 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 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= 0.537 Angle : 0.851 7.815 4325 Z= 0.500 Chirality : 0.048 0.244 540 Planarity : 0.005 0.034 522 Dihedral : 14.047 70.242 1092 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP B 313 HIS 0.008 0.002 HIS A 120 PHE 0.023 0.002 PHE B 429 TYR 0.015 0.002 TYR B 298 ARG 0.004 0.001 ARG A 208 *********************** 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 : 0.340 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 129 ASN cc_start: 0.8272 (t0) cc_final: 0.7950 (p0) 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: 0.1497 time to fit residues: 22.6651 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.198144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.165568 restraints weight = 5252.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.171171 restraints weight = 2751.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.172691 restraints weight = 1741.788| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3163 Z= 0.222 Angle : 0.712 7.619 4325 Z= 0.349 Chirality : 0.038 0.109 540 Planarity : 0.004 0.029 522 Dihedral : 5.238 53.634 501 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.95 % Allowed : 18.69 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.40), residues: 408 helix: 0.76 (0.27), residues: 336 sheet: None (None), residues: 0 loop : -3.68 (0.63), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.006 0.002 HIS A 120 PHE 0.014 0.001 PHE A 148 TYR 0.011 0.001 TYR B 16 ARG 0.002 0.000 ARG A 110 *********************** 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 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8433 (t80) cc_final: 0.8076 (t80) REVERT: A 102 LYS cc_start: 0.8353 (mttt) cc_final: 0.7862 (ttmt) REVERT: A 132 GLN cc_start: 0.8341 (mm110) cc_final: 0.7711 (mm-40) REVERT: B 329 MET cc_start: 0.8238 (ttm) cc_final: 0.7999 (ttm) outliers start: 9 outliers final: 4 residues processed: 107 average time/residue: 0.1312 time to fit residues: 17.4414 Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4258 r_free = 0.4258 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.121092 restraints weight = 6135.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.125586 restraints weight = 3327.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126946 restraints weight = 2081.913| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3163 Z= 0.207 Angle : 0.704 9.070 4325 Z= 0.339 Chirality : 0.039 0.113 540 Planarity : 0.004 0.028 522 Dihedral : 5.590 54.343 501 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.93 % Allowed : 24.26 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.42), residues: 408 helix: 1.93 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -3.28 (0.62), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.007 0.003 HIS A 120 PHE 0.012 0.001 PHE A 127 TYR 0.014 0.001 TYR B 351 ARG 0.003 0.000 ARG B 380 *********************** 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 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8470 (t80) cc_final: 0.8148 (t80) REVERT: A 47 ASN cc_start: 0.8352 (t0) cc_final: 0.8103 (t0) REVERT: A 102 LYS cc_start: 0.7965 (mttt) cc_final: 0.7359 (ttmt) REVERT: A 104 GLU cc_start: 0.6372 (mp0) cc_final: 0.6157 (mp0) REVERT: B 296 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7656 (t80) REVERT: B 298 TYR cc_start: 0.8395 (t80) cc_final: 0.6445 (t80) REVERT: B 329 MET cc_start: 0.8362 (ttm) cc_final: 0.8006 (ttm) REVERT: B 383 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8002 (mm-40) REVERT: B 396 MET cc_start: 0.7248 (mmm) cc_final: 0.6898 (mtt) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.1260 time to fit residues: 16.5260 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN 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 362 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 443 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.148885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.115596 restraints weight = 6294.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.117741 restraints weight = 3482.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.119574 restraints weight = 2605.156| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3163 Z= 0.261 Angle : 0.742 13.152 4325 Z= 0.363 Chirality : 0.041 0.124 540 Planarity : 0.004 0.033 522 Dihedral : 5.564 57.020 501 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 8.85 % Allowed : 22.95 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 408 helix: 2.00 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -2.99 (0.64), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.007 0.002 HIS A 120 PHE 0.009 0.001 PHE B 417 TYR 0.017 0.002 TYR B 351 ARG 0.002 0.000 ARG A 31 *********************** 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 125 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8522 (ptp) cc_final: 0.7991 (ppp) REVERT: A 47 ASN cc_start: 0.8361 (t0) cc_final: 0.8127 (t0) REVERT: A 102 LYS cc_start: 0.8097 (mttt) cc_final: 0.7667 (ttmt) REVERT: B 296 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 298 TYR cc_start: 0.8528 (t80) cc_final: 0.7882 (t80) REVERT: B 329 MET cc_start: 0.8448 (ttm) cc_final: 0.8101 (ttm) REVERT: B 396 MET cc_start: 0.7387 (mmm) cc_final: 0.6964 (mtt) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 0.1102 time to fit residues: 16.0398 Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 129 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 15 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110387 restraints weight = 6259.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114796 restraints weight = 3347.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.117706 restraints weight = 2327.991| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3163 Z= 0.194 Angle : 0.707 13.038 4325 Z= 0.338 Chirality : 0.039 0.128 540 Planarity : 0.004 0.036 522 Dihedral : 5.410 56.997 501 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.90 % Allowed : 30.82 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.42), residues: 408 helix: 2.10 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -3.19 (0.60), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.006 0.002 HIS A 120 PHE 0.012 0.001 PHE A 148 TYR 0.018 0.001 TYR B 351 ARG 0.001 0.000 ARG A 208 *********************** 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 120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8389 (ptp) cc_final: 0.7841 (ppp) REVERT: A 47 ASN cc_start: 0.8465 (t0) cc_final: 0.8168 (t0) REVERT: A 50 GLN cc_start: 0.7240 (pt0) cc_final: 0.6916 (pt0) REVERT: A 100 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8240 (mtmm) REVERT: A 102 LYS cc_start: 0.8109 (mttt) cc_final: 0.7704 (ttmt) REVERT: B 286 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8030 (tt) REVERT: B 296 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7643 (t80) REVERT: B 298 TYR cc_start: 0.8669 (t80) cc_final: 0.6490 (t80) REVERT: B 329 MET cc_start: 0.8482 (ttm) cc_final: 0.8109 (ttm) REVERT: B 347 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 383 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8114 (mm-40) REVERT: B 396 MET cc_start: 0.7423 (mmm) cc_final: 0.6884 (mtt) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.1180 time to fit residues: 16.6936 Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 12 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.152246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118278 restraints weight = 6304.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120623 restraints weight = 3428.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.122232 restraints weight = 2520.770| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3163 Z= 0.184 Angle : 0.721 13.305 4325 Z= 0.336 Chirality : 0.040 0.175 540 Planarity : 0.004 0.056 522 Dihedral : 5.383 58.978 501 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.26 % Allowed : 32.46 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.42), residues: 408 helix: 2.14 (0.27), residues: 338 sheet: None (None), residues: 0 loop : -3.12 (0.60), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.006 0.002 HIS A 120 PHE 0.015 0.001 PHE B 435 TYR 0.011 0.001 TYR B 351 ARG 0.001 0.000 ARG A 189 *********************** 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 118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8460 (ptp) cc_final: 0.7845 (ppp) REVERT: A 47 ASN cc_start: 0.8415 (t0) cc_final: 0.8091 (t0) REVERT: A 50 GLN cc_start: 0.7271 (pt0) cc_final: 0.6962 (pt0) REVERT: A 92 ASP cc_start: 0.9112 (m-30) cc_final: 0.8859 (m-30) REVERT: A 100 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8224 (mtmm) REVERT: A 102 LYS cc_start: 0.8082 (mttt) cc_final: 0.7497 (ttmt) REVERT: B 286 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 298 TYR cc_start: 0.8551 (t80) cc_final: 0.6350 (t80) REVERT: B 329 MET cc_start: 0.8366 (ttm) cc_final: 0.7972 (ttm) REVERT: B 365 THR cc_start: 0.8415 (p) cc_final: 0.8090 (t) REVERT: B 379 LEU cc_start: 0.8186 (tt) cc_final: 0.7983 (tt) REVERT: B 383 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8204 (mm110) REVERT: B 396 MET cc_start: 0.7444 (mmm) cc_final: 0.6967 (mtt) REVERT: B 400 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7454 (tt) outliers start: 13 outliers final: 5 residues processed: 110 average time/residue: 0.1165 time to fit residues: 16.1670 Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN 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 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 0 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4241 r_free = 0.4241 target = 0.150511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117214 restraints weight = 6336.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118484 restraints weight = 3585.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120548 restraints weight = 2781.763| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3163 Z= 0.209 Angle : 0.727 11.853 4325 Z= 0.349 Chirality : 0.041 0.153 540 Planarity : 0.004 0.050 522 Dihedral : 5.321 58.595 501 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.57 % Allowed : 33.44 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.41), residues: 408 helix: 2.15 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -3.17 (0.59), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.005 0.001 HIS A 120 PHE 0.014 0.001 PHE B 435 TYR 0.013 0.001 TYR B 351 ARG 0.001 0.000 ARG A 31 *********************** 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 119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8439 (ptp) cc_final: 0.7820 (ppp) REVERT: A 47 ASN cc_start: 0.8441 (t0) cc_final: 0.8172 (t0) REVERT: A 50 GLN cc_start: 0.7322 (pt0) cc_final: 0.7034 (pt0) REVERT: A 75 PRO cc_start: 0.7915 (Cg_exo) cc_final: 0.7688 (Cg_endo) REVERT: A 92 ASP cc_start: 0.9151 (m-30) cc_final: 0.8908 (m-30) REVERT: A 100 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8289 (mtmm) REVERT: A 102 LYS cc_start: 0.8086 (mttt) cc_final: 0.7432 (ttmt) REVERT: A 149 ASP cc_start: 0.8596 (m-30) cc_final: 0.7456 (t0) REVERT: B 286 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 296 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7678 (t80) REVERT: B 298 TYR cc_start: 0.8506 (t80) cc_final: 0.6492 (t80) REVERT: B 396 MET cc_start: 0.7421 (mmm) cc_final: 0.6920 (mtt) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.1166 time to fit residues: 16.2980 Evaluate side-chains 112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 129 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 37 ILE 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 313 TRP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 3 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.154680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.121389 restraints weight = 6292.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123044 restraints weight = 3541.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124926 restraints weight = 2739.024| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3163 Z= 0.186 Angle : 0.745 13.378 4325 Z= 0.350 Chirality : 0.043 0.396 540 Planarity : 0.004 0.056 522 Dihedral : 5.160 58.768 501 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.25 % Allowed : 34.43 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.41), residues: 408 helix: 2.27 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -3.16 (0.60), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 105 HIS 0.005 0.002 HIS A 120 PHE 0.018 0.001 PHE A 41 TYR 0.019 0.001 TYR B 351 ARG 0.001 0.000 ARG A 189 *********************** 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 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8436 (ptp) cc_final: 0.7821 (ppp) REVERT: A 47 ASN cc_start: 0.8313 (t0) cc_final: 0.7995 (t0) REVERT: A 75 PRO cc_start: 0.7953 (Cg_exo) cc_final: 0.7736 (Cg_endo) REVERT: A 100 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8172 (mtmm) REVERT: A 102 LYS cc_start: 0.7979 (mttt) cc_final: 0.7664 (ttpt) REVERT: B 286 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 298 TYR cc_start: 0.8508 (t80) cc_final: 0.7591 (t80) REVERT: B 396 MET cc_start: 0.7427 (mmm) cc_final: 0.7020 (mtt) REVERT: B 400 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7530 (tt) outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.1018 time to fit residues: 14.8622 Evaluate side-chains 114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN 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 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 438 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** 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 = 0.4263 r_free = 0.4263 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.118655 restraints weight = 6294.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120166 restraints weight = 3510.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.122485 restraints weight = 2650.980| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3163 Z= 0.219 Angle : 0.779 12.391 4325 Z= 0.377 Chirality : 0.045 0.412 540 Planarity : 0.005 0.056 522 Dihedral : 5.319 57.747 501 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.41), residues: 408 helix: 2.17 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -3.05 (0.61), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 105 HIS 0.005 0.002 HIS A 120 PHE 0.018 0.001 PHE A 41 TYR 0.016 0.001 TYR B 351 ARG 0.001 0.000 ARG B 380 *********************** 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 122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8413 (ptp) cc_final: 0.7786 (ppp) REVERT: A 47 ASN cc_start: 0.8252 (t0) cc_final: 0.7958 (t0) REVERT: A 75 PRO cc_start: 0.7804 (Cg_exo) cc_final: 0.7578 (Cg_endo) REVERT: A 102 LYS cc_start: 0.8017 (mttt) cc_final: 0.7560 (ttpt) REVERT: A 133 LEU cc_start: 0.7715 (tp) cc_final: 0.7409 (tp) REVERT: B 286 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8102 (tt) REVERT: B 298 TYR cc_start: 0.8557 (t80) cc_final: 0.6499 (t80) REVERT: B 396 MET cc_start: 0.7485 (mmm) cc_final: 0.6972 (mtt) REVERT: B 429 PHE cc_start: 0.7884 (t80) cc_final: 0.7594 (t80) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.1198 time to fit residues: 17.2279 Evaluate side-chains 117 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 129 ASN 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 324 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 411 VAL 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 3 optimal weight: 0.0980 chunk 28 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** 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 = 0.4291 r_free = 0.4291 target = 0.154483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.121674 restraints weight = 6151.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.122861 restraints weight = 3431.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.125316 restraints weight = 2638.557| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3163 Z= 0.208 Angle : 0.802 11.819 4325 Z= 0.380 Chirality : 0.044 0.401 540 Planarity : 0.005 0.056 522 Dihedral : 5.203 59.472 501 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.26 % Allowed : 37.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.41), residues: 408 helix: 2.12 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -2.97 (0.62), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 105 HIS 0.005 0.002 HIS A 120 PHE 0.019 0.001 PHE A 41 TYR 0.009 0.001 TYR B 16 ARG 0.001 0.000 ARG B 380 ********************** 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 119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8399 (ptp) cc_final: 0.7768 (ppp) REVERT: A 47 ASN cc_start: 0.8266 (t0) cc_final: 0.8016 (t0) REVERT: A 102 LYS cc_start: 0.7926 (mttt) cc_final: 0.7598 (ttpt) REVERT: A 133 LEU cc_start: 0.7672 (tp) cc_final: 0.7453 (tp) REVERT: B 286 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8024 (tt) REVERT: B 400 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7417 (tt) REVERT: B 403 ILE cc_start: 0.8384 (mm) cc_final: 0.7807 (tp) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.1207 time to fit residues: 16.4257 Evaluate side-chains 115 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN 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 324 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 383 GLN Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 411 VAL 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 20 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.154516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121452 restraints weight = 6218.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.123267 restraints weight = 3428.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.125455 restraints weight = 2548.367| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3163 Z= 0.206 Angle : 0.802 13.584 4325 Z= 0.380 Chirality : 0.044 0.392 540 Planarity : 0.005 0.054 522 Dihedral : 5.131 59.510 501 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.25 % Allowed : 36.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.42), residues: 408 helix: 2.15 (0.27), residues: 344 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 105 HIS 0.014 0.004 HIS A 99 PHE 0.019 0.001 PHE A 41 TYR 0.009 0.001 TYR B 16 ARG 0.002 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.52 seconds wall clock time: 23 minutes 19.97 seconds (1399.97 seconds total)