Starting phenix.real_space_refine on Tue Feb 11 04:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_27581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_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/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_27581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_27581.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_27581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnv_27581/02_2025/8dnv_27581.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.55, per 1000 atoms: 0.85 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 472.7 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: 0.40 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: 1.20 Time building geometry restraints manager: 1.16 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: 0.00 - 2.28: 5674 2.28 - 4.55: 58 4.55 - 6.83: 13 6.83 - 9.11: 1 9.11 - 11.39: 1 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 3.040 nonbonded pdb=" OG SER A 197 " pdb=" OE1 GLU A 210 " model vdw 2.285 3.040 nonbonded pdb=" O PRO A 17 " pdb=" NZ LYS A 117 " model vdw 2.304 3.120 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 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.110 Process input model: 14.810 Find NCS groups from input model: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.436 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: 0.1912 time to fit residues: 12.2667 Evaluate side-chains 39 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127384 restraints weight = 4746.556| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.05 r_work: 0.3442 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0874 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= 0.211 Angle : 0.541 11.181 5747 Z= 0.264 Chirality : 0.039 0.140 678 Planarity : 0.005 0.043 704 Dihedral : 3.801 17.738 571 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 4.00 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.37), residues: 525 helix: 2.31 (0.26), residues: 385 sheet: -1.83 (1.55), residues: 12 loop : -0.93 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.008 0.001 PHE A 252 TYR 0.007 0.001 TYR A 263 ARG 0.006 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 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: B 12 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.6359 (mmp-170) REVERT: A 20 GLN cc_start: 0.7699 (tt0) cc_final: 0.7028 (pt0) REVERT: A 143 MET cc_start: 0.7027 (mtt) cc_final: 0.6766 (mtt) REVERT: A 208 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 307 MET cc_start: 0.7444 (mtt) cc_final: 0.7146 (mmm) REVERT: A 465 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7243 (mm-40) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.1788 time to fit residues: 11.2791 Evaluate side-chains 46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128293 restraints weight = 4817.166| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.07 r_work: 0.3421 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1087 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= 0.203 Angle : 0.519 10.311 5747 Z= 0.253 Chirality : 0.038 0.138 678 Planarity : 0.005 0.043 704 Dihedral : 3.765 17.777 571 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 6.22 % Favored : 93.11 % 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: 2.25 (0.37), residues: 525 helix: 2.35 (0.26), residues: 386 sheet: -1.87 (1.57), residues: 12 loop : -0.92 (0.51), 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 0.010 0.001 PHE A 312 TYR 0.005 0.001 TYR A 285 ARG 0.009 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 to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.630 Fit side-chains REVERT: A 20 GLN cc_start: 0.7603 (tt0) cc_final: 0.7035 (pt0) REVERT: A 65 MET cc_start: 0.8157 (mtm) cc_final: 0.7855 (mtp) REVERT: A 208 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 307 MET cc_start: 0.7512 (mtt) cc_final: 0.7198 (mmm) REVERT: A 464 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: A 465 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7261 (mm-40) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1796 time to fit residues: 11.3984 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.163944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127428 restraints weight = 4766.893| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.06 r_work: 0.3445 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1262 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= 0.195 Angle : 0.504 9.409 5747 Z= 0.246 Chirality : 0.038 0.137 678 Planarity : 0.004 0.042 704 Dihedral : 3.730 17.535 571 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 6.44 % Favored : 92.89 % 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: 2.32 (0.37), residues: 525 helix: 2.42 (0.26), residues: 386 sheet: -1.69 (1.61), residues: 12 loop : -0.98 (0.51), 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 0.009 0.001 PHE A 312 TYR 0.005 0.001 TYR A 364 ARG 0.008 0.000 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 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.445 Fit side-chains REVERT: A 20 GLN cc_start: 0.7588 (tt0) cc_final: 0.7168 (pt0) REVERT: A 25 LYS cc_start: 0.8304 (tptt) cc_final: 0.8031 (ttpp) REVERT: A 65 MET cc_start: 0.8046 (mtm) cc_final: 0.7740 (mtp) REVERT: A 205 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7511 (mmt180) REVERT: A 208 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 307 MET cc_start: 0.7494 (mtt) cc_final: 0.7293 (mmm) REVERT: A 464 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: A 465 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7201 (mm-40) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1857 time to fit residues: 11.0234 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.162180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126107 restraints weight = 4886.675| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.04 r_work: 0.3428 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1355 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 : 0.496 8.856 5747 Z= 0.246 Chirality : 0.038 0.135 678 Planarity : 0.005 0.046 704 Dihedral : 3.720 17.546 571 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.11 % Allowed : 7.11 % Favored : 91.78 % 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: 2.46 (0.26), residues: 386 sheet: -1.68 (1.58), residues: 12 loop : -1.07 (0.51), 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 0.009 0.001 PHE A 312 TYR 0.005 0.001 TYR A 285 ARG 0.009 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 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.489 Fit side-chains REVERT: A 20 GLN cc_start: 0.7620 (tt0) cc_final: 0.7218 (pt0) REVERT: A 25 LYS cc_start: 0.8294 (tptt) cc_final: 0.8006 (ttpp) REVERT: A 205 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7538 (mmt180) REVERT: A 208 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 464 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: A 465 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7146 (mm-40) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.1944 time to fit residues: 12.8287 Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.162753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126757 restraints weight = 4785.750| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.02 r_work: 0.3423 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1442 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= 0.197 Angle : 0.495 8.697 5747 Z= 0.244 Chirality : 0.038 0.135 678 Planarity : 0.005 0.047 704 Dihedral : 3.700 17.467 571 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 2.33 (0.37), residues: 525 helix: 2.45 (0.26), residues: 386 sheet: -1.44 (1.61), residues: 12 loop : -1.10 (0.51), 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 0.009 0.001 PHE A 156 TYR 0.005 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 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.445 Fit side-chains REVERT: A 20 GLN cc_start: 0.7649 (tt0) cc_final: 0.7277 (pt0) REVERT: A 25 LYS cc_start: 0.8259 (tptt) cc_final: 0.7962 (ttpp) REVERT: A 208 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 307 MET cc_start: 0.7151 (mmm) cc_final: 0.6768 (mmm) REVERT: A 464 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 465 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7160 (mm-40) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1851 time to fit residues: 12.1059 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 39 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.163610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127121 restraints weight = 4827.635| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.06 r_work: 0.3433 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4246 Z= 0.212 Angle : 0.503 8.947 5747 Z= 0.247 Chirality : 0.038 0.136 678 Planarity : 0.005 0.049 704 Dihedral : 3.707 17.532 571 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 8.22 % Favored : 91.11 % 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: 2.34 (0.37), residues: 525 helix: 2.45 (0.26), residues: 386 sheet: -1.23 (1.65), residues: 12 loop : -1.11 (0.51), 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 360 PHE 0.009 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.011 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 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.494 Fit side-chains REVERT: A 20 GLN cc_start: 0.7657 (tt0) cc_final: 0.7316 (pt0) REVERT: A 25 LYS cc_start: 0.8344 (tptt) cc_final: 0.8061 (ttpp) REVERT: A 208 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 307 MET cc_start: 0.7229 (mmm) cc_final: 0.6823 (mmm) REVERT: A 464 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: A 465 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7160 (mm-40) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1876 time to fit residues: 12.3110 Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.161745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125701 restraints weight = 4781.314| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.02 r_work: 0.3431 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4246 Z= 0.227 Angle : 0.509 9.189 5747 Z= 0.250 Chirality : 0.038 0.136 678 Planarity : 0.005 0.049 704 Dihedral : 3.721 17.712 571 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 8.67 % Favored : 90.44 % 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: 2.30 (0.37), residues: 525 helix: 2.43 (0.26), residues: 386 sheet: -1.15 (1.67), residues: 12 loop : -1.13 (0.52), 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 156 TYR 0.006 0.001 TYR A 285 ARG 0.011 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 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.513 Fit side-chains REVERT: A 20 GLN cc_start: 0.7644 (tt0) cc_final: 0.7303 (pt0) REVERT: A 25 LYS cc_start: 0.8349 (tptt) cc_final: 0.8062 (ttpp) REVERT: A 65 MET cc_start: 0.8160 (mtm) cc_final: 0.7853 (mtp) REVERT: A 205 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7523 (mmt180) REVERT: A 208 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 464 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 465 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7127 (mm-40) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.1996 time to fit residues: 13.4673 Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.161396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125264 restraints weight = 4800.325| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.02 r_work: 0.3424 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1599 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= 0.235 Angle : 0.517 9.248 5747 Z= 0.254 Chirality : 0.039 0.136 678 Planarity : 0.005 0.048 704 Dihedral : 3.734 17.833 571 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 2.24 (0.37), residues: 525 helix: 2.43 (0.26), residues: 381 sheet: -1.15 (1.67), residues: 12 loop : -1.22 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.011 0.001 PHE A 312 TYR 0.007 0.001 TYR A 285 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 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.456 Fit side-chains REVERT: A 20 GLN cc_start: 0.7637 (tt0) cc_final: 0.7203 (pt0) REVERT: A 25 LYS cc_start: 0.8350 (tptt) cc_final: 0.8064 (ttpp) REVERT: A 65 MET cc_start: 0.8175 (mtm) cc_final: 0.7869 (mtp) REVERT: A 205 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7519 (mmt180) REVERT: A 208 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 307 MET cc_start: 0.7215 (mmm) cc_final: 0.6831 (mmm) REVERT: A 464 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 465 GLN cc_start: 0.7352 (mm-40) cc_final: 0.7113 (mm-40) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1894 time to fit residues: 11.8356 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 6 optimal weight: 0.0270 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.164942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129004 restraints weight = 4739.590| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.01 r_work: 0.3463 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1626 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= 0.160 Angle : 0.487 7.997 5747 Z= 0.238 Chirality : 0.038 0.138 678 Planarity : 0.004 0.047 704 Dihedral : 3.640 17.150 571 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.18 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: 2.45 (0.37), residues: 525 helix: 2.59 (0.26), residues: 381 sheet: -1.12 (1.67), residues: 12 loop : -1.14 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.001 0.001 HIS A 360 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR A 137 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 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.477 Fit side-chains REVERT: A 20 GLN cc_start: 0.7644 (tt0) cc_final: 0.7328 (pt0) REVERT: A 25 LYS cc_start: 0.8351 (tptt) cc_final: 0.8067 (ttpp) REVERT: A 65 MET cc_start: 0.8111 (mtm) cc_final: 0.7804 (mtp) REVERT: A 208 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 307 MET cc_start: 0.7205 (mmm) cc_final: 0.6834 (mmm) REVERT: A 464 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 465 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7054 (mm-40) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.1800 time to fit residues: 11.9622 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 445 THR 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 50 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.165862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127921 restraints weight = 4932.710| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.18 r_work: 0.3400 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1673 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= 0.250 Angle : 0.524 9.092 5747 Z= 0.259 Chirality : 0.039 0.137 678 Planarity : 0.005 0.051 704 Dihedral : 3.720 17.421 571 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 2.29 (0.37), residues: 525 helix: 2.47 (0.26), residues: 381 sheet: -1.18 (1.66), residues: 12 loop : -1.19 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.002 HIS A 218 PHE 0.010 0.001 PHE A 312 TYR 0.008 0.001 TYR A 285 ARG 0.011 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.09 seconds wall clock time: 43 minutes 54.86 seconds (2634.86 seconds total)