Starting phenix.real_space_refine on Tue Feb 13 04:28:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_30074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_30074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_30074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_30074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/02_2024/6m49_30074_updated.pdb" } 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 Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.35, per 1000 atoms: 0.76 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 - 3.50 Amino acid : False - 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: 1.60 Conformation dependent library (CDL) restraints added in 643.8 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 19 through 50 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 73 through 95 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 27 through 46 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 283 through 304 Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 313 through 337 removed outlier: 4.115A pdb=" N GLY B 332 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 335 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 359 through 369 removed outlier: 4.968A pdb=" N LEU B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 389 through 407 Processing helix chain 'B' and resid 412 through 448 removed outlier: 4.347A pdb=" N THR B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 245 hydrogen bonds defined for protein. 675 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: 0.81 Time building geometry restraints manager: 1.53 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: 98.18 - 105.36: 49 105.36 - 112.54: 1763 112.54 - 119.72: 989 119.72 - 126.91: 1483 126.91 - 134.09: 41 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: 62 2.64 - 3.21: 3488 3.21 - 3.77: 4769 3.77 - 4.34: 5981 4.34 - 4.90: 9342 Nonbonded interactions: 23642 Sorted by model distance: nonbonded pdb=" O GLN A 52 " pdb=" NE2 GLN A 52 " model vdw 2.079 2.520 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 2.440 nonbonded pdb=" O PHE A 163 " pdb=" OG1 THR A 166 " model vdw 2.298 2.440 nonbonded pdb=" O PRO B 287 " pdb=" OG1 THR B 291 " model vdw 2.299 2.440 ... (remaining 23637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 1.820 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- 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= 0.542 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 fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.312 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: 0.1542 time to fit residues: 23.2616 Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3163 Z= 0.194 Angle : 0.693 7.444 4325 Z= 0.336 Chirality : 0.037 0.110 540 Planarity : 0.004 0.025 522 Dihedral : 5.217 53.722 501 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.61 % Allowed : 18.03 % 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: -0.18 (0.41), residues: 408 helix: 0.67 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -3.49 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.007 0.002 HIS A 120 PHE 0.014 0.001 PHE A 148 TYR 0.012 0.001 TYR B 16 ARG 0.002 0.000 ARG B 380 *********************** 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 119 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8325 (t80) cc_final: 0.8053 (t80) REVERT: A 47 ASN cc_start: 0.8559 (t0) cc_final: 0.8236 (t0) REVERT: A 102 LYS cc_start: 0.8136 (mttt) cc_final: 0.7850 (ttmt) REVERT: A 132 GLN cc_start: 0.8246 (mm110) cc_final: 0.7649 (mm-40) REVERT: B 380 ARG cc_start: 0.6969 (ttt180) cc_final: 0.6740 (ttt180) REVERT: B 396 MET cc_start: 0.7136 (mmm) cc_final: 0.6600 (mtt) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.1252 time to fit residues: 17.4417 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4621 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= 0.186 Angle : 0.671 9.440 4325 Z= 0.322 Chirality : 0.038 0.113 540 Planarity : 0.004 0.028 522 Dihedral : 5.445 54.028 501 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.57 % Allowed : 22.95 % 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 (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: 1.40 (0.43), residues: 408 helix: 1.77 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.05 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.007 0.002 HIS A 120 PHE 0.013 0.001 PHE A 127 TYR 0.013 0.001 TYR B 351 ARG 0.002 0.000 ARG A 103 *********************** 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 114 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8408 (t80) cc_final: 0.8172 (t80) REVERT: A 47 ASN cc_start: 0.8397 (t0) cc_final: 0.8138 (t0) REVERT: A 102 LYS cc_start: 0.7557 (mttt) cc_final: 0.7266 (mtmt) REVERT: B 296 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 298 TYR cc_start: 0.8186 (t80) cc_final: 0.7629 (t80) REVERT: B 344 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6993 (p0) REVERT: B 383 GLN cc_start: 0.8230 (mm110) cc_final: 0.7963 (mm110) REVERT: B 396 MET cc_start: 0.7240 (mmm) cc_final: 0.6699 (mtt) REVERT: B 432 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8100 (pp30) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.1242 time to fit residues: 16.1710 Evaluate side-chains 97 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 50 GLN 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 289 VAL Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 344 ASN 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 36 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.5009 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= 0.193 Angle : 0.666 12.854 4325 Z= 0.320 Chirality : 0.038 0.110 540 Planarity : 0.004 0.032 522 Dihedral : 5.209 52.186 501 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.90 % Allowed : 26.89 % Favored : 67.21 % 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: 1.65 (0.43), residues: 408 helix: 1.93 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.81 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.007 0.002 HIS A 120 PHE 0.008 0.001 PHE A 148 TYR 0.014 0.001 TYR B 351 ARG 0.001 0.000 ARG A 208 *********************** 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 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.365 Fit side-chains REVERT: A 29 MET cc_start: 0.8448 (ptp) cc_final: 0.7937 (ppp) REVERT: A 47 ASN cc_start: 0.8411 (t0) cc_final: 0.8008 (t0) REVERT: A 50 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: A 72 TRP cc_start: 0.6820 (m-10) cc_final: 0.6584 (m-10) REVERT: A 102 LYS cc_start: 0.7587 (mttt) cc_final: 0.7108 (ttmt) REVERT: B 296 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 298 TYR cc_start: 0.8214 (t80) cc_final: 0.7550 (t80) REVERT: B 344 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7045 (p0) REVERT: B 383 GLN cc_start: 0.8334 (mm110) cc_final: 0.8050 (mm110) REVERT: B 432 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8146 (pp30) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.1164 time to fit residues: 14.9098 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 50 GLN 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 201 ILE Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 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 22 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3163 Z= 0.180 Angle : 0.663 13.451 4325 Z= 0.316 Chirality : 0.038 0.117 540 Planarity : 0.004 0.033 522 Dihedral : 5.135 52.416 501 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.57 % Allowed : 28.52 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.43), residues: 408 helix: 1.99 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.73 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.007 0.002 HIS A 120 PHE 0.008 0.001 PHE A 148 TYR 0.013 0.001 TYR B 351 ARG 0.001 0.000 ARG A 103 *********************** 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 117 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.355 Fit side-chains REVERT: A 29 MET cc_start: 0.8381 (ptp) cc_final: 0.7850 (ppp) REVERT: A 47 ASN cc_start: 0.8361 (t0) cc_final: 0.8048 (t0) REVERT: A 92 ASP cc_start: 0.9159 (m-30) cc_final: 0.8862 (m-30) REVERT: A 104 GLU cc_start: 0.6355 (mp0) cc_final: 0.6148 (tp30) REVERT: B 296 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 298 TYR cc_start: 0.8214 (t80) cc_final: 0.7468 (t80) REVERT: B 344 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7113 (p0) REVERT: B 383 GLN cc_start: 0.8349 (mm110) cc_final: 0.8055 (mm110) REVERT: B 396 MET cc_start: 0.7003 (mmm) cc_final: 0.6738 (mtt) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1197 time to fit residues: 16.1728 Evaluate side-chains 104 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 331 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5523 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= 0.192 Angle : 0.667 12.270 4325 Z= 0.316 Chirality : 0.038 0.122 540 Planarity : 0.004 0.038 522 Dihedral : 5.085 53.907 501 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 8.20 % Allowed : 26.23 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.43), residues: 408 helix: 2.04 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.54 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 105 HIS 0.006 0.002 HIS A 120 PHE 0.017 0.001 PHE A 127 TYR 0.012 0.001 TYR B 351 ARG 0.002 0.000 ARG B 380 *********************** 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 121 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8460 (ptp) cc_final: 0.7906 (ppp) REVERT: A 47 ASN cc_start: 0.8460 (t0) cc_final: 0.8204 (t0) REVERT: A 72 TRP cc_start: 0.6779 (m-10) cc_final: 0.6549 (m-10) REVERT: A 92 ASP cc_start: 0.9169 (m-30) cc_final: 0.8858 (m-30) REVERT: A 100 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8431 (mtmm) REVERT: A 144 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7665 (tp) REVERT: B 286 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 296 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 298 TYR cc_start: 0.8283 (t80) cc_final: 0.7486 (t80) REVERT: B 344 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 383 GLN cc_start: 0.8447 (mm110) cc_final: 0.8139 (mm110) REVERT: B 396 MET cc_start: 0.7050 (mmm) cc_final: 0.6690 (mtt) outliers start: 25 outliers final: 15 residues processed: 109 average time/residue: 0.1178 time to fit residues: 16.3118 Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 344 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0060 chunk 25 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 99 HIS ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5771 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= 0.177 Angle : 0.691 13.203 4325 Z= 0.325 Chirality : 0.038 0.132 540 Planarity : 0.004 0.039 522 Dihedral : 4.982 53.994 501 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.25 % Allowed : 29.51 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.42), residues: 408 helix: 2.03 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -2.75 (0.63), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 105 HIS 0.007 0.002 HIS A 120 PHE 0.012 0.001 PHE A 127 TYR 0.013 0.001 TYR B 351 ARG 0.002 0.000 ARG B 380 *********************** 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 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.420 Fit side-chains REVERT: A 29 MET cc_start: 0.8427 (ptp) cc_final: 0.7829 (ppp) REVERT: A 47 ASN cc_start: 0.8511 (t0) cc_final: 0.8201 (t0) REVERT: A 72 TRP cc_start: 0.6791 (m-10) cc_final: 0.6547 (m-10) REVERT: A 92 ASP cc_start: 0.9191 (m-30) cc_final: 0.8868 (m-30) REVERT: A 100 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8375 (mtmm) REVERT: A 104 GLU cc_start: 0.6287 (mp0) cc_final: 0.6073 (mp0) REVERT: B 286 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8084 (tt) REVERT: B 298 TYR cc_start: 0.8257 (t80) cc_final: 0.7323 (t80) REVERT: B 344 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 383 GLN cc_start: 0.8435 (mm110) cc_final: 0.8126 (mm110) REVERT: B 396 MET cc_start: 0.7042 (mmm) cc_final: 0.6655 (mtt) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.1362 time to fit residues: 18.8910 Evaluate side-chains 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 166 THR 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 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 ASN 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 26 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5981 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= 0.189 Angle : 0.709 13.390 4325 Z= 0.334 Chirality : 0.039 0.177 540 Planarity : 0.004 0.036 522 Dihedral : 4.975 55.490 501 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.23 % Allowed : 28.20 % Favored : 65.57 % 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: 1.92 (0.43), residues: 408 helix: 2.03 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.43 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 145 HIS 0.006 0.002 HIS A 120 PHE 0.009 0.001 PHE B 436 TYR 0.017 0.001 TYR B 351 ARG 0.001 0.000 ARG B 380 *********************** 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 118 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.301 Fit side-chains REVERT: A 29 MET cc_start: 0.8425 (ptp) cc_final: 0.7808 (ppp) REVERT: A 47 ASN cc_start: 0.8601 (t0) cc_final: 0.8306 (t0) REVERT: A 72 TRP cc_start: 0.6843 (m-10) cc_final: 0.6580 (m-10) REVERT: A 92 ASP cc_start: 0.9166 (m-30) cc_final: 0.8828 (m-30) REVERT: A 100 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8412 (mtmm) REVERT: A 102 LYS cc_start: 0.7311 (ttpt) cc_final: 0.6990 (ttmt) REVERT: A 104 GLU cc_start: 0.6390 (mp0) cc_final: 0.6132 (mp0) REVERT: B 286 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 296 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 298 TYR cc_start: 0.8371 (t80) cc_final: 0.7529 (t80) REVERT: B 344 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7231 (p0) REVERT: B 383 GLN cc_start: 0.8596 (mm110) cc_final: 0.8284 (mm-40) REVERT: B 396 MET cc_start: 0.7097 (mmm) cc_final: 0.6659 (mtt) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.1175 time to fit residues: 15.7272 Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 50 GLN 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 296 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3163 Z= 0.189 Angle : 0.713 12.250 4325 Z= 0.334 Chirality : 0.039 0.158 540 Planarity : 0.004 0.035 522 Dihedral : 4.996 55.123 501 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.25 % Allowed : 30.82 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.42), residues: 408 helix: 2.04 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.34 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 145 HIS 0.007 0.002 HIS A 120 PHE 0.007 0.001 PHE B 417 TYR 0.015 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 109 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.360 Fit side-chains REVERT: A 29 MET cc_start: 0.8428 (ptp) cc_final: 0.7791 (ppp) REVERT: A 47 ASN cc_start: 0.8513 (t0) cc_final: 0.8259 (t0) REVERT: A 92 ASP cc_start: 0.9175 (m-30) cc_final: 0.8841 (m-30) REVERT: A 100 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8386 (mtmm) REVERT: A 102 LYS cc_start: 0.7333 (ttpt) cc_final: 0.7055 (ttpt) REVERT: A 104 GLU cc_start: 0.6322 (mp0) cc_final: 0.6045 (mp0) REVERT: B 286 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 298 TYR cc_start: 0.8387 (t80) cc_final: 0.7544 (t80) REVERT: B 344 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7284 (p0) REVERT: B 383 GLN cc_start: 0.8574 (mm110) cc_final: 0.8252 (mm110) REVERT: B 396 MET cc_start: 0.7153 (mmm) cc_final: 0.6692 (mtt) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1203 time to fit residues: 15.3801 Evaluate side-chains 106 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 50 GLN 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 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 352 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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** A 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 3163 Z= 0.306 Angle : 0.781 14.323 4325 Z= 0.378 Chirality : 0.042 0.153 540 Planarity : 0.004 0.033 522 Dihedral : 5.476 59.905 501 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 (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: 1.46 (0.41), residues: 408 helix: 1.72 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.70 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 105 HIS 0.007 0.002 HIS A 120 PHE 0.020 0.002 PHE A 41 TYR 0.013 0.002 TYR B 298 ARG 0.002 0.000 ARG A 208 ********************** 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 fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8428 (ptp) cc_final: 0.7792 (ppp) REVERT: A 47 ASN cc_start: 0.8556 (t0) cc_final: 0.8283 (t0) REVERT: A 104 GLU cc_start: 0.6746 (mp0) cc_final: 0.6512 (mp0) REVERT: A 133 LEU cc_start: 0.7766 (tp) cc_final: 0.7396 (tp) REVERT: B 286 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 296 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 298 TYR cc_start: 0.8491 (t80) cc_final: 0.6783 (t80) REVERT: B 344 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 347 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 383 GLN cc_start: 0.8674 (mm110) cc_final: 0.8354 (mm110) REVERT: B 396 MET cc_start: 0.7158 (mmm) cc_final: 0.6706 (mtt) outliers start: 19 outliers final: 15 residues processed: 106 average time/residue: 0.1197 time to fit residues: 15.9047 Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 50 GLN 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 325 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 352 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 403 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 28 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** A 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.170766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.140640 restraints weight = 6424.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.141718 restraints weight = 3427.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.143631 restraints weight = 2636.749| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3163 Z= 0.202 Angle : 0.758 13.283 4325 Z= 0.351 Chirality : 0.039 0.165 540 Planarity : 0.004 0.034 522 Dihedral : 5.250 58.344 501 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.25 % Allowed : 31.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.42), residues: 408 helix: 1.96 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.22 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 145 HIS 0.007 0.002 HIS A 120 PHE 0.020 0.001 PHE A 41 TYR 0.011 0.001 TYR B 351 ARG 0.001 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.71 seconds wall clock time: 20 minutes 20.57 seconds (1220.57 seconds total)