Starting phenix.real_space_refine on Fri Apr 5 17:18:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnv_27581/04_2024/8dnv_27581.pdb" } resolution = 3.03 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= 0.004 sd= 0.045 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 26 5.16 5 C 2747 2.51 5 N 673 2.21 5 O 711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4157 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 486 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3420 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.02, per 1000 atoms: 0.73 Number of scatterers: 4157 At special positions: 0 Unit cell: (92.4, 80.85, 79.8, 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 26 16.00 O 711 8.00 N 673 7.00 C 2747 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: 1.85 Conformation dependent library (CDL) restraints added in 928.1 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 980 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 75.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 95 Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.542A pdb=" N VAL A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 15' Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 172 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.572A pdb=" N ALA A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.933A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 288 through 312 removed outlier: 3.601A pdb=" N ARG A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 409 through 439 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.544A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.585A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 633 1.31 - 1.44: 1118 1.44 - 1.56: 2452 1.56 - 1.68: 0 1.68 - 1.81: 43 Bond restraints: 4246 Sorted by residual: bond pdb=" C SER A 443 " pdb=" O SER A 443 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" CA GLY A 446 " pdb=" C GLY A 446 " ideal model delta sigma weight residual 1.516 1.483 0.033 1.12e-02 7.97e+03 8.69e+00 bond pdb=" C ARG A 66 " pdb=" O ARG A 66 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.15e-02 7.56e+03 8.09e+00 bond pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.30e-02 5.92e+03 7.40e+00 bond pdb=" CA MET C 86 " pdb=" C MET C 86 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.31e+00 ... (remaining 4241 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.06: 116 107.06 - 113.79: 2427 113.79 - 120.51: 1704 120.51 - 127.24: 1464 127.24 - 133.97: 36 Bond angle restraints: 5747 Sorted by residual: angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 109.58 104.56 5.02 1.29e+00 6.01e-01 1.51e+01 angle pdb=" N MET A 65 " pdb=" CA MET A 65 " pdb=" C MET A 65 " ideal model delta sigma weight residual 113.38 108.82 4.56 1.23e+00 6.61e-01 1.37e+01 angle pdb=" C VAL A 67 " pdb=" CA VAL A 67 " pdb=" CB VAL A 67 " ideal model delta sigma weight residual 112.14 107.59 4.55 1.35e+00 5.49e-01 1.13e+01 angle pdb=" N LEU A 69 " pdb=" CA LEU A 69 " pdb=" C LEU A 69 " ideal model delta sigma weight residual 113.30 109.06 4.24 1.34e+00 5.57e-01 1.00e+01 angle pdb=" N GLU A 464 " pdb=" CA GLU A 464 " pdb=" CB GLU A 464 " ideal model delta sigma weight residual 110.28 114.86 -4.58 1.55e+00 4.16e-01 8.74e+00 ... (remaining 5742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2321 17.34 - 34.68: 168 34.68 - 52.02: 16 52.02 - 69.37: 3 69.37 - 86.71: 5 Dihedral angle restraints: 2513 sinusoidal: 985 harmonic: 1528 Sorted by residual: dihedral pdb=" CA LYS A 171 " pdb=" C LYS A 171 " pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual -180.00 -165.28 -14.72 0 5.00e+00 4.00e-02 8.67e+00 dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -165.79 -14.21 0 5.00e+00 4.00e-02 8.07e+00 ... (remaining 2510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 415 0.030 - 0.060: 182 0.060 - 0.089: 60 0.089 - 0.119: 16 0.119 - 0.149: 5 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 441 " pdb=" N ILE A 441 " pdb=" C ILE A 441 " pdb=" CB ILE A 441 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA GLU A 464 " pdb=" N GLU A 464 " pdb=" C GLU A 464 " pdb=" CB GLU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB ILE A 380 " pdb=" CA ILE A 380 " pdb=" CG1 ILE A 380 " pdb=" CG2 ILE A 380 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 675 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 386 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 387 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 418 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 83 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.024 5.00e-02 4.00e+02 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1050 2.80 - 3.33: 4254 3.33 - 3.85: 7033 3.85 - 4.38: 7675 4.38 - 4.90: 13988 Nonbonded interactions: 34000 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.276 2.440 nonbonded pdb=" OG SER A 197 " pdb=" OE1 GLU A 210 " model vdw 2.285 2.440 nonbonded pdb=" O PRO A 17 " pdb=" NZ LYS A 117 " model vdw 2.304 2.520 nonbonded pdb=" O ILE A 460 " pdb=" OE1 GLU A 464 " model vdw 2.362 3.040 nonbonded pdb=" NH2 ARG A 236 " pdb=" O PRO A 240 " model vdw 2.376 2.520 ... (remaining 33995 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 individual isotropic 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: 0.700 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: 3.690 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.004 0.048 4246 Z= 0.243 Angle : 0.593 11.387 5747 Z= 0.317 Chirality : 0.039 0.149 678 Planarity : 0.005 0.045 704 Dihedral : 11.811 86.707 1533 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.82 (0.37), residues: 525 helix: 1.93 (0.26), residues: 389 sheet: -1.99 (1.47), residues: 12 loop : -0.79 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.002 HIS A 360 PHE 0.014 0.001 PHE A 252 TYR 0.004 0.001 TYR A 285 ARG 0.004 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.483 Fit side-chains REVERT: A 18 GLU cc_start: 0.7361 (pm20) cc_final: 0.7159 (pm20) REVERT: A 20 GLN cc_start: 0.7493 (tt0) cc_final: 0.6930 (pt0) REVERT: A 77 MET cc_start: 0.8344 (mmp) cc_final: 0.8140 (mmt) REVERT: A 154 GLN cc_start: 0.7879 (mt0) cc_final: 0.7461 (mt0) REVERT: A 208 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 307 MET cc_start: 0.7183 (mtt) cc_final: 0.6846 (mmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1903 time to fit residues: 12.1904 Evaluate side-chains 39 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4246 Z= 0.232 Angle : 0.548 12.326 5747 Z= 0.266 Chirality : 0.039 0.139 678 Planarity : 0.005 0.043 704 Dihedral : 3.801 17.841 571 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 4.22 % Favored : 95.11 % 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: 2.16 (0.37), residues: 525 helix: 2.27 (0.26), residues: 386 sheet: -1.69 (1.57), residues: 12 loop : -0.93 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.002 HIS A 360 PHE 0.008 0.001 PHE A 252 TYR 0.008 0.001 TYR A 263 ARG 0.004 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.7438 (tt0) cc_final: 0.6745 (pt0) REVERT: A 77 MET cc_start: 0.8397 (mmp) cc_final: 0.8171 (mmt) REVERT: A 143 MET cc_start: 0.6890 (mtt) cc_final: 0.6640 (mtt) REVERT: A 208 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 307 MET cc_start: 0.7187 (mtt) cc_final: 0.6945 (mmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1716 time to fit residues: 10.8078 Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4246 Z= 0.189 Angle : 0.509 10.691 5747 Z= 0.246 Chirality : 0.038 0.135 678 Planarity : 0.005 0.042 704 Dihedral : 3.736 17.564 571 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 6.44 % Favored : 92.67 % 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: 2.34 (0.37), residues: 525 helix: 2.43 (0.26), residues: 386 sheet: -1.65 (1.57), residues: 12 loop : -0.95 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.010 0.001 PHE A 312 TYR 0.005 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.489 Fit side-chains REVERT: A 20 GLN cc_start: 0.7420 (tt0) cc_final: 0.6793 (pt0) REVERT: A 65 MET cc_start: 0.7639 (mtm) cc_final: 0.7347 (mtp) REVERT: A 77 MET cc_start: 0.8347 (mmp) cc_final: 0.8141 (mmt) REVERT: A 208 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 307 MET cc_start: 0.7256 (mtt) cc_final: 0.7003 (mmm) REVERT: A 464 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6324 (mp0) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1586 time to fit residues: 10.1327 Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4246 Z= 0.167 Angle : 0.484 9.235 5747 Z= 0.237 Chirality : 0.037 0.135 678 Planarity : 0.004 0.042 704 Dihedral : 3.682 17.306 571 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 7.56 % Favored : 91.56 % 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: 2.44 (0.37), residues: 525 helix: 2.51 (0.26), residues: 386 sheet: -1.49 (1.55), residues: 12 loop : -0.98 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.007 0.001 PHE A 156 TYR 0.005 0.001 TYR A 364 ARG 0.012 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.442 Fit side-chains REVERT: A 20 GLN cc_start: 0.7408 (tt0) cc_final: 0.6837 (pt0) REVERT: A 25 LYS cc_start: 0.8185 (tptt) cc_final: 0.7962 (ttpp) REVERT: A 77 MET cc_start: 0.8337 (mmp) cc_final: 0.8117 (mmt) REVERT: A 208 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 464 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6208 (mp0) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1687 time to fit residues: 10.5567 Evaluate side-chains 47 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4246 Z= 0.209 Angle : 0.498 9.320 5747 Z= 0.244 Chirality : 0.038 0.136 678 Planarity : 0.005 0.047 704 Dihedral : 3.691 17.403 571 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 8.22 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.37), residues: 525 helix: 2.48 (0.26), residues: 386 sheet: -1.42 (1.54), residues: 12 loop : -1.05 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 PHE 0.010 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.510 Fit side-chains REVERT: A 20 GLN cc_start: 0.7410 (tt0) cc_final: 0.6848 (pt0) REVERT: A 91 MET cc_start: 0.7049 (mmp) cc_final: 0.6820 (mmm) REVERT: A 208 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 307 MET cc_start: 0.6871 (mmm) cc_final: 0.6478 (mmm) REVERT: A 464 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6316 (mp0) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1932 time to fit residues: 11.8123 Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4246 Z= 0.173 Angle : 0.482 8.502 5747 Z= 0.236 Chirality : 0.037 0.134 678 Planarity : 0.004 0.047 704 Dihedral : 3.641 17.120 571 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.67 % Allowed : 9.33 % Favored : 90.00 % 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: 2.49 (0.37), residues: 525 helix: 2.57 (0.26), residues: 386 sheet: -1.26 (1.54), residues: 12 loop : -1.06 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 156 TYR 0.004 0.001 TYR A 285 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.575 Fit side-chains REVERT: A 20 GLN cc_start: 0.7412 (tt0) cc_final: 0.6895 (pt0) REVERT: A 77 MET cc_start: 0.8306 (mmt) cc_final: 0.7926 (mmt) REVERT: A 208 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 464 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6278 (mp0) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.1919 time to fit residues: 11.7421 Evaluate side-chains 47 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4246 Z= 0.271 Angle : 0.530 10.423 5747 Z= 0.260 Chirality : 0.039 0.139 678 Planarity : 0.005 0.050 704 Dihedral : 3.769 18.104 571 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 9.11 % Favored : 90.00 % 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: 2.24 (0.37), residues: 525 helix: 2.39 (0.26), residues: 386 sheet: -1.10 (1.59), residues: 12 loop : -1.19 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.002 HIS A 360 PHE 0.010 0.001 PHE A 312 TYR 0.008 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.462 Fit side-chains REVERT: A 20 GLN cc_start: 0.7422 (tt0) cc_final: 0.6893 (pt0) REVERT: A 77 MET cc_start: 0.8276 (mmt) cc_final: 0.7949 (mmt) REVERT: A 208 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 464 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6276 (mp0) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1770 time to fit residues: 10.9091 Evaluate side-chains 45 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4246 Z= 0.229 Angle : 0.508 9.727 5747 Z= 0.250 Chirality : 0.038 0.137 678 Planarity : 0.005 0.047 704 Dihedral : 3.759 17.839 571 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.67 % Allowed : 9.78 % Favored : 89.56 % 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: 2.28 (0.37), residues: 525 helix: 2.42 (0.26), residues: 386 sheet: -0.92 (1.62), residues: 12 loop : -1.20 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 PHE 0.008 0.001 PHE A 252 TYR 0.007 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.490 Fit side-chains REVERT: A 20 GLN cc_start: 0.7415 (tt0) cc_final: 0.6892 (pt0) REVERT: A 77 MET cc_start: 0.8458 (mmt) cc_final: 0.8087 (mmt) REVERT: A 208 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 464 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6353 (mp0) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1822 time to fit residues: 10.9072 Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.0030 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4246 Z= 0.149 Angle : 0.474 7.494 5747 Z= 0.233 Chirality : 0.037 0.143 678 Planarity : 0.004 0.047 704 Dihedral : 3.611 16.835 571 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.44 % Allowed : 10.89 % Favored : 88.67 % 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: 2.55 (0.37), residues: 525 helix: 2.61 (0.26), residues: 386 sheet: -0.91 (1.61), residues: 12 loop : -1.07 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.001 0.001 HIS A 218 PHE 0.009 0.001 PHE A 156 TYR 0.006 0.001 TYR A 137 ARG 0.010 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.447 Fit side-chains REVERT: A 20 GLN cc_start: 0.7439 (tt0) cc_final: 0.6943 (pt0) REVERT: A 77 MET cc_start: 0.8420 (mmp) cc_final: 0.7953 (mmt) REVERT: A 208 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 307 MET cc_start: 0.6900 (mmm) cc_final: 0.6526 (mmm) REVERT: A 464 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6343 (mp0) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1744 time to fit residues: 10.3151 Evaluate side-chains 45 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4246 Z= 0.196 Angle : 0.499 8.220 5747 Z= 0.244 Chirality : 0.038 0.135 678 Planarity : 0.004 0.048 704 Dihedral : 3.626 17.029 571 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.44 % Allowed : 11.33 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.36), residues: 525 helix: 2.57 (0.26), residues: 381 sheet: -1.03 (1.59), residues: 12 loop : -1.15 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 PHE 0.009 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.477 Fit side-chains REVERT: A 20 GLN cc_start: 0.7437 (tt0) cc_final: 0.6944 (pt0) REVERT: A 77 MET cc_start: 0.8455 (mmp) cc_final: 0.8048 (mmt) REVERT: A 208 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 464 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6406 (mp0) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1650 time to fit residues: 9.1358 Evaluate side-chains 42 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127065 restraints weight = 4782.695| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.02 r_work: 0.3450 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4246 Z= 0.176 Angle : 0.492 8.523 5747 Z= 0.239 Chirality : 0.038 0.136 678 Planarity : 0.004 0.047 704 Dihedral : 3.595 16.821 571 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 10.89 % Favored : 88.44 % 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: 2.49 (0.36), residues: 525 helix: 2.61 (0.26), residues: 381 sheet: -1.01 (1.59), residues: 12 loop : -1.10 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 312 TYR 0.005 0.001 TYR A 137 ARG 0.010 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.66 seconds wall clock time: 24 minutes 27.78 seconds (1467.78 seconds total)