Starting phenix.real_space_refine on Fri Dec 27 09:38:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.map" model { file = "/net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bim_44593/12_2024/9bim_44593.cif" } resolution = 3.67 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= 0.000 sd= 0.207 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 20 5.16 5 C 2665 2.51 5 N 605 2.21 5 O 702 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: 3992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3962 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HC6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.76 Number of scatterers: 3992 At special positions: 0 Unit cell: (58.8, 83.16, 84, 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 20 16.00 O 702 8.00 N 605 7.00 C 2665 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 1.2 seconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 73.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.737A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.092A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.611A pdb=" N MET A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 157 removed outlier: 3.501A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ARG A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.671A pdb=" N SER A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 208 removed outlier: 3.969A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.714A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.321A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 298 removed outlier: 3.529A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.604A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 426 removed outlier: 3.631A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.757A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.544A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 262 hydrogen bonds defined for protein. 777 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: 1.07 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1153 1.34 - 1.46: 753 1.46 - 1.57: 2165 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 4106 Sorted by residual: bond pdb=" CAS HC6 A 701 " pdb=" OBD HC6 A 701 " ideal model delta sigma weight residual 1.389 1.430 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" CAB HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.500 1.459 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" CAC HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" CAD HC6 A 701 " pdb=" OBC HC6 A 701 " ideal model delta sigma weight residual 1.389 1.423 -0.034 2.00e-02 2.50e+03 2.98e+00 bond pdb=" CAX HC6 A 701 " pdb=" NAW HC6 A 701 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 4101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5478 2.04 - 4.07: 104 4.07 - 6.11: 22 6.11 - 8.14: 9 8.14 - 10.18: 1 Bond angle restraints: 5614 Sorted by residual: angle pdb=" CA TYR A 175 " pdb=" CB TYR A 175 " pdb=" CG TYR A 175 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" N GLY A 179 " pdb=" CA GLY A 179 " pdb=" C GLY A 179 " ideal model delta sigma weight residual 113.18 120.19 -7.01 2.37e+00 1.78e-01 8.75e+00 angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" C VAL A 178 " pdb=" N GLY A 179 " pdb=" CA GLY A 179 " ideal model delta sigma weight residual 121.41 115.93 5.48 1.96e+00 2.60e-01 7.81e+00 angle pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " ideal model delta sigma weight residual 112.00 118.13 -6.13 2.20e+00 2.07e-01 7.76e+00 ... (remaining 5609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 2101 14.67 - 29.33: 179 29.33 - 44.00: 61 44.00 - 58.66: 4 58.66 - 73.33: 7 Dihedral angle restraints: 2352 sinusoidal: 869 harmonic: 1483 Sorted by residual: dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA MET A 114 " pdb=" C MET A 114 " pdb=" N LEU A 115 " pdb=" CA LEU A 115 " ideal model delta harmonic sigma weight residual 180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N LEU A 8 " pdb=" CA LEU A 8 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 476 0.045 - 0.090: 132 0.090 - 0.136: 33 0.136 - 0.181: 5 0.181 - 0.226: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE A 157 " pdb=" CA ILE A 157 " pdb=" CG1 ILE A 157 " pdb=" CG2 ILE A 157 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 644 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 175 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 175 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 175 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 175 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 175 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 175 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 418 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO A 419 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 116 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 117 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.018 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 944 2.79 - 3.32: 3830 3.32 - 3.84: 6747 3.84 - 4.37: 7356 4.37 - 4.90: 13195 Nonbonded interactions: 32072 Sorted by model distance: nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.259 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP A 309 " pdb=" NZ LYS A 311 " model vdw 2.361 3.120 nonbonded pdb=" O ALA A 60 " pdb=" OG SER A 346 " model vdw 2.450 3.040 nonbonded pdb=" OH TYR A 305 " pdb=" OE1 GLU A 315 " model vdw 2.458 3.040 ... (remaining 32067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.044 4106 Z= 0.249 Angle : 0.745 10.179 5614 Z= 0.365 Chirality : 0.045 0.226 647 Planarity : 0.005 0.040 680 Dihedral : 13.024 73.329 1414 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.35), residues: 512 helix: 0.49 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.97 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.002 0.001 HIS A 162 PHE 0.021 0.002 PHE A 258 TYR 0.026 0.002 TYR A 175 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.423 Fit side-chains REVERT: A 106 MET cc_start: 0.7221 (mmt) cc_final: 0.6655 (mmt) REVERT: A 269 TYR cc_start: 0.8135 (m-10) cc_final: 0.7855 (m-10) REVERT: A 484 MET cc_start: 0.8321 (tmm) cc_final: 0.7986 (ttt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2019 time to fit residues: 6.5293 Evaluate side-chains 22 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.7296 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.209 Angle : 0.571 7.613 5614 Z= 0.285 Chirality : 0.040 0.138 647 Planarity : 0.004 0.026 680 Dihedral : 7.892 55.516 591 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.48 % Allowed : 6.04 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.37), residues: 512 helix: 1.10 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.000 HIS A 162 PHE 0.010 0.001 PHE A 244 TYR 0.022 0.001 TYR A 67 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.363 Fit side-chains REVERT: A 106 MET cc_start: 0.7241 (mmt) cc_final: 0.6605 (mmt) REVERT: A 269 TYR cc_start: 0.8153 (m-10) cc_final: 0.7832 (m-80) REVERT: A 484 MET cc_start: 0.8410 (tmm) cc_final: 0.7648 (ttt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1939 time to fit residues: 6.1655 Evaluate side-chains 22 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 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: 0.7576 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4106 Z= 0.173 Angle : 0.531 6.564 5614 Z= 0.263 Chirality : 0.039 0.135 647 Planarity : 0.003 0.024 680 Dihedral : 6.338 40.909 591 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 8.21 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.36 (0.38), residues: 512 helix: 1.44 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -0.42 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 244 TYR 0.022 0.001 TYR A 175 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.428 Fit side-chains REVERT: A 109 LYS cc_start: 0.7265 (pttm) cc_final: 0.6930 (ptpt) REVERT: A 269 TYR cc_start: 0.8154 (m-10) cc_final: 0.7718 (m-80) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.2073 time to fit residues: 7.1767 Evaluate side-chains 26 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4106 Z= 0.215 Angle : 0.551 8.587 5614 Z= 0.273 Chirality : 0.039 0.146 647 Planarity : 0.004 0.025 680 Dihedral : 6.418 43.079 591 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.97 % Allowed : 9.66 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.38), residues: 512 helix: 1.46 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.36 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 56 TYR 0.022 0.001 TYR A 67 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.450 Fit side-chains REVERT: A 109 LYS cc_start: 0.7326 (pttm) cc_final: 0.7060 (ptpt) REVERT: A 269 TYR cc_start: 0.8220 (m-10) cc_final: 0.7724 (m-80) REVERT: A 484 MET cc_start: 0.8479 (tmm) cc_final: 0.7700 (ttt) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.2226 time to fit residues: 7.1254 Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 overall best weight: 0.5312 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.169 Angle : 0.527 7.682 5614 Z= 0.258 Chirality : 0.038 0.140 647 Planarity : 0.003 0.026 680 Dihedral : 5.896 38.374 591 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.42 % Allowed : 8.70 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.38), residues: 512 helix: 1.66 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.40 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.402 Fit side-chains REVERT: A 109 LYS cc_start: 0.7313 (pttm) cc_final: 0.7051 (ptpt) REVERT: A 139 MET cc_start: 0.7065 (mmm) cc_final: 0.5321 (mtp) REVERT: A 187 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 484 MET cc_start: 0.8437 (tmm) cc_final: 0.7615 (ttt) outliers start: 10 outliers final: 5 residues processed: 32 average time/residue: 0.1898 time to fit residues: 7.9050 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7596 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4106 Z= 0.178 Angle : 0.519 7.831 5614 Z= 0.258 Chirality : 0.039 0.140 647 Planarity : 0.004 0.026 680 Dihedral : 5.695 36.788 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.90 % Allowed : 7.97 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.71 (0.38), residues: 512 helix: 1.70 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.369 Fit side-chains REVERT: A 187 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7881 (m) outliers start: 12 outliers final: 6 residues processed: 31 average time/residue: 0.1958 time to fit residues: 7.8039 Evaluate side-chains 31 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.0020 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3746 ------------------------------------------------------------------------------- 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: 0.7556 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4106 Z= 0.144 Angle : 0.503 7.421 5614 Z= 0.248 Chirality : 0.037 0.137 647 Planarity : 0.003 0.028 680 Dihedral : 5.281 32.464 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.42 % Allowed : 8.45 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.38), residues: 512 helix: 1.91 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.09 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.023 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.423 Fit side-chains REVERT: A 139 MET cc_start: 0.7060 (mmm) cc_final: 0.5243 (mtp) REVERT: A 187 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 484 MET cc_start: 0.8490 (tmm) cc_final: 0.7808 (ttt) outliers start: 10 outliers final: 5 residues processed: 31 average time/residue: 0.2016 time to fit residues: 8.0722 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.197 Angle : 0.533 7.843 5614 Z= 0.261 Chirality : 0.039 0.140 647 Planarity : 0.004 0.029 680 Dihedral : 5.484 34.912 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 9.18 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 512 helix: 1.73 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.27 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.021 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.371 Fit side-chains REVERT: A 484 MET cc_start: 0.8464 (tmm) cc_final: 0.7767 (ttt) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.1942 time to fit residues: 7.5499 Evaluate side-chains 32 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4106 Z= 0.156 Angle : 0.519 8.389 5614 Z= 0.254 Chirality : 0.038 0.138 647 Planarity : 0.003 0.029 680 Dihedral : 5.205 31.962 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 9.90 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.96 (0.38), residues: 512 helix: 1.89 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.25 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.023 0.001 TYR A 175 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.444 Fit side-chains REVERT: A 106 MET cc_start: 0.7044 (mmt) cc_final: 0.6302 (mmt) REVERT: A 139 MET cc_start: 0.7073 (mmm) cc_final: 0.5243 (ttp) REVERT: A 358 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7579 (mtp) REVERT: A 484 MET cc_start: 0.8457 (tmm) cc_final: 0.7905 (ttt) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.2199 time to fit residues: 7.3281 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7586 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4106 Z= 0.177 Angle : 0.526 7.734 5614 Z= 0.257 Chirality : 0.038 0.138 647 Planarity : 0.004 0.030 680 Dihedral : 5.249 32.707 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 9.42 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.91 (0.38), residues: 512 helix: 1.85 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.25 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.022 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.442 Fit side-chains REVERT: A 139 MET cc_start: 0.7088 (mmm) cc_final: 0.5268 (ttp) REVERT: A 358 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: A 484 MET cc_start: 0.8462 (tmm) cc_final: 0.7753 (ttt) outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 0.2172 time to fit residues: 7.5532 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108649 restraints weight = 4141.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111245 restraints weight = 2754.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113494 restraints weight = 2142.462| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4106 Z= 0.213 Angle : 0.549 8.155 5614 Z= 0.269 Chirality : 0.039 0.140 647 Planarity : 0.004 0.030 680 Dihedral : 5.536 35.925 591 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.69 % Allowed : 10.14 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.78 (0.38), residues: 512 helix: 1.72 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.20 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 406 HIS 0.002 0.000 HIS A 162 PHE 0.009 0.001 PHE A 56 TYR 0.021 0.001 TYR A 175 ARG 0.007 0.001 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1091.76 seconds wall clock time: 21 minutes 16.11 seconds (1276.11 seconds total)