Starting phenix.real_space_refine on Wed Mar 5 22:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9x_51160/03_2025/9g9x_51160.cif" } resolution = 3.13 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= 0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 22 5.16 5 C 2630 2.51 5 N 622 2.21 5 O 678 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-5624/modules/chem_data/mon_lib" Total number of atoms: 3955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1906 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' K': 3, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B Time building chain proxies: 3.54, per 1000 atoms: 0.90 Number of scatterers: 3955 At special positions: 0 Unit cell: (60.736, 70.72, 89.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 22 16.00 O 678 8.00 N 622 7.00 C 2630 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: 0.96 Conformation dependent library (CDL) restraints added in 421.0 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 908 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.237A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 3.598A pdb=" N GLN A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 143 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 removed outlier: 3.713A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.113A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.601A pdb=" N GLU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix removed outlier: 3.597A pdb=" N GLN B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 143 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.115A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 314 hydrogen bonds defined for protein. 924 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: 1.02 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 612 1.32 - 1.44: 1146 1.44 - 1.56: 2262 1.56 - 1.68: 0 1.68 - 1.80: 34 Bond restraints: 4054 Sorted by residual: bond pdb=" CBC Y01 B 302 " pdb=" OAW Y01 B 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CBC Y01 A 302 " pdb=" OAW Y01 A 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB ILE B 200 " pdb=" CG2 ILE B 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB ILE A 200 " pdb=" CG2 ILE A 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 4049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4924 1.08 - 2.17: 496 2.17 - 3.25: 86 3.25 - 4.34: 12 4.34 - 5.42: 16 Bond angle restraints: 5534 Sorted by residual: angle pdb=" N ARG A 79 " pdb=" CA ARG A 79 " pdb=" C ARG A 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.75e+00 angle pdb=" N ARG B 79 " pdb=" CA ARG B 79 " pdb=" C ARG B 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.74e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 118.60 -5.42 2.37e+00 1.78e-01 5.24e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 118.57 -5.39 2.37e+00 1.78e-01 5.18e+00 angle pdb=" N GLU B 32 " pdb=" CA GLU B 32 " pdb=" C GLU B 32 " ideal model delta sigma weight residual 109.81 114.60 -4.79 2.21e+00 2.05e-01 4.69e+00 ... (remaining 5529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2360 17.21 - 34.41: 132 34.41 - 51.62: 22 51.62 - 68.82: 4 68.82 - 86.02: 2 Dihedral angle restraints: 2520 sinusoidal: 1100 harmonic: 1420 Sorted by residual: dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 277 0.032 - 0.063: 231 0.063 - 0.095: 99 0.095 - 0.126: 31 0.126 - 0.158: 12 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 647 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 173 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.68e+00 pdb=" C ILE A 173 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 173 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 174 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 20 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU B 20 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 20 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 21 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 173 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ILE B 173 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 174 " 0.015 2.00e-02 2.50e+03 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.95: 1809 2.95 - 3.50: 4785 3.50 - 4.05: 7006 4.05 - 4.59: 10684 4.59 - 5.14: 14537 Nonbonded interactions: 38821 Sorted by model distance: nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.404 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.404 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.420 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.421 3.040 nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.423 3.040 ... (remaining 38816 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 252 or resid 301 through 302)) selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.150 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.007 0.045 4054 Z= 0.461 Angle : 0.749 5.423 5534 Z= 0.442 Chirality : 0.052 0.158 650 Planarity : 0.006 0.026 668 Dihedral : 11.299 86.025 1612 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.34), residues: 480 helix: -0.43 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -1.24 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 78 HIS 0.001 0.001 HIS B 180 PHE 0.019 0.002 PHE A 202 TYR 0.023 0.004 TYR A 85 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.395 Fit side-chains REVERT: A 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6434 (ttt-90) REVERT: A 130 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 135 LEU cc_start: 0.7284 (tp) cc_final: 0.6593 (mp) REVERT: A 249 MET cc_start: 0.5337 (ttt) cc_final: 0.5109 (ttp) REVERT: B 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6435 (ttt-90) REVERT: B 130 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6552 (tm-30) REVERT: B 135 LEU cc_start: 0.7280 (tp) cc_final: 0.6592 (mp) REVERT: B 249 MET cc_start: 0.5342 (ttt) cc_final: 0.5115 (ttp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2024 time to fit residues: 16.1300 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115359 restraints weight = 3792.413| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.39 r_work: 0.3038 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.201 Angle : 0.516 4.964 5534 Z= 0.279 Chirality : 0.039 0.157 650 Planarity : 0.003 0.016 668 Dihedral : 5.450 50.527 818 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 4.12 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.39), residues: 480 helix: 1.93 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.42 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 184 HIS 0.001 0.000 HIS B 72 PHE 0.012 0.001 PHE A 109 TYR 0.014 0.001 TYR A 85 ARG 0.004 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.438 Fit side-chains REVERT: A 135 LEU cc_start: 0.6857 (tp) cc_final: 0.6266 (mp) REVERT: B 135 LEU cc_start: 0.6872 (tp) cc_final: 0.6284 (mp) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1962 time to fit residues: 12.9100 Evaluate side-chains 46 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.176901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114649 restraints weight = 3812.885| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.35 r_work: 0.2977 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4054 Z= 0.271 Angle : 0.525 5.105 5534 Z= 0.281 Chirality : 0.041 0.153 650 Planarity : 0.003 0.018 668 Dihedral : 5.558 49.549 818 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.55 % Allowed : 6.19 % Favored : 92.27 % 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: 3.19 (0.40), residues: 480 helix: 2.34 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.17 (0.84), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.010 0.001 PHE A 109 TYR 0.012 0.001 TYR A 85 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.390 Fit side-chains REVERT: A 135 LEU cc_start: 0.6923 (tp) cc_final: 0.6336 (mp) REVERT: B 135 LEU cc_start: 0.6923 (tp) cc_final: 0.6338 (mp) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.1822 time to fit residues: 13.8471 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.180159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118438 restraints weight = 3820.122| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.36 r_work: 0.3095 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4054 Z= 0.163 Angle : 0.461 5.009 5534 Z= 0.244 Chirality : 0.038 0.150 650 Planarity : 0.002 0.017 668 Dihedral : 5.294 47.430 818 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % 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: 3.70 (0.40), residues: 480 helix: 2.70 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.33 (0.88), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.010 0.001 PHE A 109 TYR 0.009 0.001 TYR A 85 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.394 Fit side-chains REVERT: A 135 LEU cc_start: 0.7071 (tp) cc_final: 0.6473 (mp) REVERT: B 135 LEU cc_start: 0.7080 (tp) cc_final: 0.6480 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.2050 time to fit residues: 12.4900 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 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 = 0.3978 r_free = 0.3978 target = 0.178948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116914 restraints weight = 3921.661| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.35 r_work: 0.2955 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.200 Angle : 0.477 5.076 5534 Z= 0.254 Chirality : 0.039 0.156 650 Planarity : 0.003 0.018 668 Dihedral : 5.283 45.075 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.80 % Allowed : 6.96 % Favored : 91.24 % 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: 3.86 (0.40), residues: 480 helix: 2.87 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.14 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.010 0.001 PHE A 109 TYR 0.009 0.001 TYR A 85 ARG 0.004 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.360 Fit side-chains REVERT: A 135 LEU cc_start: 0.6959 (tp) cc_final: 0.6371 (mp) REVERT: B 135 LEU cc_start: 0.6964 (tp) cc_final: 0.6376 (mp) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.1870 time to fit residues: 13.0239 Evaluate side-chains 51 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.176765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114989 restraints weight = 3816.730| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.31 r_work: 0.3054 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4054 Z= 0.185 Angle : 0.469 5.082 5534 Z= 0.248 Chirality : 0.038 0.152 650 Planarity : 0.003 0.023 668 Dihedral : 5.153 41.431 818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.29 % Allowed : 7.22 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.40), residues: 480 helix: 2.99 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.17 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.001 0.000 HIS A 180 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR B 113 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.394 Fit side-chains REVERT: A 135 LEU cc_start: 0.7027 (tp) cc_final: 0.6447 (mp) REVERT: B 135 LEU cc_start: 0.7028 (tp) cc_final: 0.6450 (mp) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.2004 time to fit residues: 12.9935 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 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 = 0.3948 r_free = 0.3948 target = 0.175735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114420 restraints weight = 3815.556| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.29 r_work: 0.3045 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.200 Angle : 0.479 5.107 5534 Z= 0.254 Chirality : 0.038 0.152 650 Planarity : 0.003 0.026 668 Dihedral : 5.093 38.303 818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.22 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.39), residues: 480 helix: 3.06 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.04 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE A 109 TYR 0.009 0.001 TYR B 113 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.433 Fit side-chains REVERT: A 135 LEU cc_start: 0.7071 (tp) cc_final: 0.6482 (mp) REVERT: B 135 LEU cc_start: 0.7072 (tp) cc_final: 0.6485 (mp) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.2251 time to fit residues: 13.7798 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114070 restraints weight = 3763.655| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.29 r_work: 0.3041 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.207 Angle : 0.479 5.125 5534 Z= 0.254 Chirality : 0.038 0.153 650 Planarity : 0.003 0.024 668 Dihedral : 5.041 37.623 818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.22 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.39), residues: 480 helix: 3.06 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.99 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR B 113 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.414 Fit side-chains REVERT: A 135 LEU cc_start: 0.7072 (tp) cc_final: 0.6467 (mp) REVERT: B 135 LEU cc_start: 0.7064 (tp) cc_final: 0.6464 (mp) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.2073 time to fit residues: 13.4024 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115333 restraints weight = 3796.969| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.31 r_work: 0.3032 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4054 Z= 0.173 Angle : 0.464 5.063 5534 Z= 0.244 Chirality : 0.037 0.153 650 Planarity : 0.003 0.024 668 Dihedral : 4.885 36.603 818 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.25 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.39), residues: 480 helix: 3.15 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.85 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.009 0.001 PHE A 109 TYR 0.008 0.001 TYR B 113 ARG 0.005 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.367 Fit side-chains REVERT: A 135 LEU cc_start: 0.7016 (tp) cc_final: 0.6437 (mp) REVERT: B 135 LEU cc_start: 0.7024 (tp) cc_final: 0.6446 (mp) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.2032 time to fit residues: 12.0992 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114923 restraints weight = 3831.341| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.32 r_work: 0.2996 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.182 Angle : 0.469 5.098 5534 Z= 0.247 Chirality : 0.038 0.151 650 Planarity : 0.003 0.022 668 Dihedral : 4.857 35.564 818 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.51 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.39), residues: 480 helix: 3.16 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.86 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 72 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR A 113 ARG 0.005 0.001 ARG A 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.372 Fit side-chains REVERT: A 135 LEU cc_start: 0.7008 (tp) cc_final: 0.6428 (mp) REVERT: B 135 LEU cc_start: 0.7004 (tp) cc_final: 0.6428 (mp) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.2158 time to fit residues: 12.5822 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.178168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117205 restraints weight = 3820.957| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.30 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4054 Z= 0.153 Angle : 0.454 5.044 5534 Z= 0.237 Chirality : 0.037 0.152 650 Planarity : 0.003 0.022 668 Dihedral : 4.717 34.066 818 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.76 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.39), residues: 480 helix: 3.24 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.84 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.001 0.000 HIS A 72 PHE 0.009 0.001 PHE B 109 TYR 0.008 0.001 TYR A 113 ARG 0.005 0.001 ARG A 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.54 seconds wall clock time: 42 minutes 47.02 seconds (2567.02 seconds total)