Starting phenix.real_space_refine on Fri Dec 27 10:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588.map" model { file = "/net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do2_27588/12_2024/8do2_27588_trim.cif" } resolution = 2.95 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= 0.003 sd= 0.049 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 28 5.16 5 C 2803 2.51 5 N 674 2.21 5 O 721 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-5532/modules/chem_data/mon_lib" Total number of atoms: 4226 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3462 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'SXU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.44, per 1000 atoms: 0.81 Number of scatterers: 4226 At special positions: 0 Unit cell: (85.05, 76.65, 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 28 16.00 O 721 8.00 N 674 7.00 C 2803 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: 1.05 Conformation dependent library (CDL) restraints added in 529.9 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 74.5% alpha, 2.8% 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 9 through 14 Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 108 through 134 Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.903A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.752A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.547A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.617A pdb=" N ALA A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 442 through 468 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 262 through 265 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.470A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 939 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: 1.34 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 943 1.33 - 1.46: 1358 1.46 - 1.59: 1970 1.59 - 1.72: 0 1.72 - 1.85: 47 Bond restraints: 4318 Sorted by residual: bond pdb=" C22 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.759 1.852 -0.093 2.00e-02 2.50e+03 2.19e+01 bond pdb=" N03 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.648 1.737 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C33 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.768 1.852 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N19 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.661 1.740 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C09 SXU A 501 " pdb=" C10 SXU A 501 " ideal model delta sigma weight residual 1.509 1.568 -0.059 2.00e-02 2.50e+03 8.72e+00 ... (remaining 4313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 5838 4.67 - 9.34: 8 9.34 - 14.01: 2 14.01 - 18.68: 1 18.68 - 23.36: 1 Bond angle restraints: 5850 Sorted by residual: angle pdb=" O21 SXU A 501 " pdb=" S20 SXU A 501 " pdb=" O29 SXU A 501 " ideal model delta sigma weight residual 117.02 93.66 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" O01 SXU A 501 " pdb=" S02 SXU A 501 " pdb=" O40 SXU A 501 " ideal model delta sigma weight residual 119.05 101.62 17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C04 SXU A 501 " pdb=" N03 SXU A 501 " pdb=" C05 SXU A 501 " ideal model delta sigma weight residual 115.30 125.30 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 110.20 114.45 -4.25 1.32e+00 5.74e-01 1.04e+01 angle pdb=" N ARG A 223 " pdb=" CA ARG A 223 " pdb=" C ARG A 223 " ideal model delta sigma weight residual 110.23 114.84 -4.61 1.45e+00 4.76e-01 1.01e+01 ... (remaining 5845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 2361 17.18 - 34.35: 185 34.35 - 51.53: 22 51.53 - 68.71: 4 68.71 - 85.88: 4 Dihedral angle restraints: 2576 sinusoidal: 1030 harmonic: 1546 Sorted by residual: dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" N ARG B 20 " pdb=" CA ARG B 20 " pdb=" CB ARG B 20 " pdb=" CG ARG B 20 " ideal model delta sinusoidal sigma weight residual 60.00 113.15 -53.15 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB MET B 47 " pdb=" CG MET B 47 " pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -108.15 48.15 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 2573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 402 0.029 - 0.057: 174 0.057 - 0.085: 80 0.085 - 0.114: 22 0.114 - 0.142: 10 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN A 288 " pdb=" N ASN A 288 " pdb=" C ASN A 288 " pdb=" CB ASN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 685 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 240 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 83 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C22 SXU A 501 " 0.010 2.00e-02 2.50e+03 9.64e-03 1.86e+00 pdb=" C23 SXU A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C24 SXU A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C25 SXU A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C26 SXU A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C27 SXU A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C28 SXU A 501 " 0.011 2.00e-02 2.50e+03 pdb=" S20 SXU A 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 950 2.78 - 3.31: 4236 3.31 - 3.84: 7269 3.84 - 4.37: 8081 4.37 - 4.90: 14578 Nonbonded interactions: 35114 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.254 3.040 nonbonded pdb=" O ARG A 236 " pdb=" ND2 ASN A 241 " model vdw 2.261 3.120 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.362 3.040 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.372 3.040 nonbonded pdb=" OH TYR A 364 " pdb=" OD2 ASP A 436 " model vdw 2.394 3.040 ... (remaining 35109 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: 0.850 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.320 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.005 0.093 4318 Z= 0.320 Angle : 0.735 23.356 5850 Z= 0.348 Chirality : 0.040 0.142 688 Planarity : 0.004 0.049 711 Dihedral : 12.560 85.884 1584 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % 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: 2.17 (0.37), residues: 531 helix: 2.26 (0.26), residues: 398 sheet: -3.75 (0.84), residues: 20 loop : -0.55 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.010 0.001 PHE B 52 TYR 0.008 0.001 TYR A 457 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.491 Fit side-chains REVERT: B 30 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6850 (mmt180) REVERT: A 294 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 368 MET cc_start: 0.7431 (tpp) cc_final: 0.7038 (tpp) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 1.6441 time to fit residues: 99.9760 Evaluate side-chains 43 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4318 Z= 0.182 Angle : 0.529 7.689 5850 Z= 0.261 Chirality : 0.039 0.157 688 Planarity : 0.004 0.048 711 Dihedral : 5.787 55.270 625 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 6.64 % Favored : 92.04 % 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: 531 helix: 2.51 (0.25), residues: 400 sheet: -3.67 (0.86), residues: 20 loop : -0.36 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.001 0.001 HIS A 360 PHE 0.007 0.001 PHE A 156 TYR 0.004 0.001 TYR A 263 ARG 0.005 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.517 Fit side-chains REVERT: B 30 ARG cc_start: 0.7120 (ttt90) cc_final: 0.6750 (mmp-170) REVERT: A 167 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 189 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: A 231 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6043 (mmp-170) REVERT: A 294 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 317 LEU cc_start: 0.8266 (mm) cc_final: 0.7748 (tp) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 1.4660 time to fit residues: 86.5506 Evaluate side-chains 53 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4318 Z= 0.185 Angle : 0.515 6.683 5850 Z= 0.255 Chirality : 0.039 0.155 688 Planarity : 0.004 0.048 711 Dihedral : 4.845 30.363 621 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.99 % Allowed : 8.19 % Favored : 89.82 % 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: 2.60 (0.37), residues: 531 helix: 2.59 (0.25), residues: 400 sheet: -3.71 (0.81), residues: 20 loop : -0.48 (0.61), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 261 TYR 0.005 0.001 TYR A 137 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.497 Fit side-chains REVERT: B 30 ARG cc_start: 0.7137 (ttt90) cc_final: 0.6776 (mmp-170) REVERT: A 91 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7659 (mmp) REVERT: A 167 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 189 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: A 231 ARG cc_start: 0.6959 (ttm-80) cc_final: 0.5937 (mmp-170) REVERT: A 311 ARG cc_start: 0.6642 (mtm180) cc_final: 0.6265 (mtt180) REVERT: A 317 LEU cc_start: 0.8282 (mm) cc_final: 0.7751 (tp) outliers start: 9 outliers final: 1 residues processed: 57 average time/residue: 1.3289 time to fit residues: 78.6394 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 0.0470 chunk 42 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4318 Z= 0.198 Angle : 0.521 6.761 5850 Z= 0.256 Chirality : 0.039 0.154 688 Planarity : 0.004 0.048 711 Dihedral : 4.598 26.741 621 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 11.50 % Favored : 87.17 % 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: 2.66 (0.37), residues: 531 helix: 2.63 (0.25), residues: 400 sheet: -3.50 (0.81), residues: 22 loop : -0.43 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.004 0.001 TYR A 173 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.501 Fit side-chains REVERT: B 30 ARG cc_start: 0.7030 (ttt90) cc_final: 0.6614 (mmp-170) REVERT: A 23 GLU cc_start: 0.6793 (pm20) cc_final: 0.6435 (tt0) REVERT: A 91 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7751 (mmp) REVERT: A 167 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 189 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 294 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7474 (tt0) REVERT: A 317 LEU cc_start: 0.8279 (mm) cc_final: 0.7740 (tp) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 1.2621 time to fit residues: 74.8739 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4318 Z= 0.204 Angle : 0.512 6.335 5850 Z= 0.252 Chirality : 0.039 0.152 688 Planarity : 0.004 0.049 711 Dihedral : 4.510 22.947 621 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.77 % Allowed : 11.50 % Favored : 86.73 % 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: 2.79 (0.37), residues: 531 helix: 2.79 (0.25), residues: 393 sheet: -3.47 (0.81), residues: 22 loop : -0.44 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.004 0.001 TYR A 302 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.482 Fit side-chains REVERT: B 30 ARG cc_start: 0.7087 (ttt90) cc_final: 0.6628 (mmp-170) REVERT: A 167 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 189 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: A 317 LEU cc_start: 0.8349 (mm) cc_final: 0.7871 (tt) outliers start: 8 outliers final: 1 residues processed: 53 average time/residue: 1.2915 time to fit residues: 71.0169 Evaluate side-chains 48 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 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: 2.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4318 Z= 0.209 Angle : 0.527 6.611 5850 Z= 0.259 Chirality : 0.039 0.151 688 Planarity : 0.004 0.048 711 Dihedral : 4.551 23.463 621 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.77 % Allowed : 12.83 % Favored : 85.40 % 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: 2.76 (0.37), residues: 531 helix: 2.76 (0.25), residues: 393 sheet: -3.44 (0.79), residues: 22 loop : -0.42 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.006 0.001 TYR A 302 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.531 Fit side-chains REVERT: B 20 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6301 (ttp80) REVERT: B 30 ARG cc_start: 0.7069 (ttt90) cc_final: 0.6624 (mmp-170) REVERT: A 23 GLU cc_start: 0.6824 (pm20) cc_final: 0.6301 (tt0) REVERT: A 100 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7144 (tp) REVERT: A 167 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 189 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: A 317 LEU cc_start: 0.8342 (mm) cc_final: 0.7880 (tt) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 1.3130 time to fit residues: 72.3909 Evaluate side-chains 51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4318 Z= 0.225 Angle : 0.528 6.599 5850 Z= 0.260 Chirality : 0.039 0.150 688 Planarity : 0.004 0.049 711 Dihedral : 4.754 25.632 621 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.77 % Allowed : 12.83 % Favored : 85.40 % 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: 2.70 (0.37), residues: 531 helix: 2.72 (0.25), residues: 393 sheet: -3.54 (0.80), residues: 22 loop : -0.47 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.009 0.001 TYR A 302 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.487 Fit side-chains REVERT: B 20 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6319 (ttp80) REVERT: B 30 ARG cc_start: 0.7039 (ttt90) cc_final: 0.6618 (mmp-170) REVERT: A 23 GLU cc_start: 0.6820 (pm20) cc_final: 0.6197 (tt0) REVERT: A 167 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 189 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: A 294 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7293 (tt0) REVERT: A 317 LEU cc_start: 0.8350 (mm) cc_final: 0.7896 (tt) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 1.3676 time to fit residues: 76.5926 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4318 Z= 0.170 Angle : 0.523 7.466 5850 Z= 0.255 Chirality : 0.038 0.149 688 Planarity : 0.004 0.048 711 Dihedral : 4.757 27.927 621 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 14.16 % Favored : 84.73 % 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: 2.78 (0.37), residues: 531 helix: 2.80 (0.25), residues: 393 sheet: -3.44 (0.81), residues: 22 loop : -0.52 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.009 0.001 TYR A 137 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.552 Fit side-chains REVERT: B 20 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6292 (ttp80) REVERT: B 30 ARG cc_start: 0.7026 (ttt90) cc_final: 0.6594 (mmp-170) REVERT: A 23 GLU cc_start: 0.6672 (pm20) cc_final: 0.6105 (tt0) REVERT: A 189 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: A 317 LEU cc_start: 0.8362 (mm) cc_final: 0.7915 (tt) REVERT: A 368 MET cc_start: 0.7605 (tpp) cc_final: 0.7338 (tpp) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 1.4107 time to fit residues: 71.6910 Evaluate side-chains 48 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4318 Z= 0.282 Angle : 0.557 7.691 5850 Z= 0.273 Chirality : 0.040 0.150 688 Planarity : 0.004 0.049 711 Dihedral : 4.951 29.876 621 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 13.50 % Favored : 84.96 % 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: 2.61 (0.37), residues: 531 helix: 2.67 (0.25), residues: 393 sheet: -3.49 (0.82), residues: 22 loop : -0.55 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.011 0.001 PHE A 261 TYR 0.012 0.001 TYR A 302 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.440 Fit side-chains REVERT: B 20 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6316 (ttp80) REVERT: B 30 ARG cc_start: 0.7037 (ttt90) cc_final: 0.6617 (mmp-170) REVERT: A 23 GLU cc_start: 0.6809 (pm20) cc_final: 0.6218 (tt0) REVERT: A 65 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7796 (mtp) REVERT: A 189 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: A 317 LEU cc_start: 0.8357 (mm) cc_final: 0.7904 (tt) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.3374 time to fit residues: 70.9583 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4318 Z= 0.209 Angle : 0.547 8.496 5850 Z= 0.265 Chirality : 0.039 0.147 688 Planarity : 0.004 0.049 711 Dihedral : 4.979 30.903 621 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.33 % Allowed : 13.72 % Favored : 84.96 % 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: 2.68 (0.37), residues: 531 helix: 2.70 (0.25), residues: 393 sheet: -3.44 (0.83), residues: 22 loop : -0.49 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.012 0.001 TYR A 302 ARG 0.006 0.001 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.447 Fit side-chains REVERT: B 20 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6258 (ttp80) REVERT: B 30 ARG cc_start: 0.7027 (ttt90) cc_final: 0.6589 (mmp-170) REVERT: A 23 GLU cc_start: 0.6773 (pm20) cc_final: 0.6167 (tt0) REVERT: A 65 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7794 (mtp) REVERT: A 189 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 317 LEU cc_start: 0.8368 (mm) cc_final: 0.7924 (tt) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 1.3175 time to fit residues: 68.5021 Evaluate side-chains 51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0670 chunk 42 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119721 restraints weight = 4487.619| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.74 r_work: 0.3237 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4318 Z= 0.163 Angle : 0.520 8.238 5850 Z= 0.254 Chirality : 0.038 0.146 688 Planarity : 0.004 0.048 711 Dihedral : 4.893 30.688 621 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.11 % Allowed : 13.94 % Favored : 84.96 % 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: 2.77 (0.37), residues: 531 helix: 2.79 (0.25), residues: 393 sheet: -3.34 (0.84), residues: 22 loop : -0.56 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.007 0.001 PHE A 423 TYR 0.013 0.001 TYR A 302 ARG 0.006 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.02 seconds wall clock time: 35 minutes 1.66 seconds (2101.66 seconds total)