Starting phenix.real_space_refine on Wed Jul 1 23:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9x_51160/07_2026/9g9x_51160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9x_51160/07_2026/9g9x_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_51160/07_2026/9g9x_51160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9x_51160/07_2026/9g9x_51160.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9x_51160/07_2026/9g9x_51160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9x_51160/07_2026/9g9x_51160.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3955 Number of models: 1 Model: "" Number of chains: 4 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: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" 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: {'ARG:plan': 3, 'GLU: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, 70 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.88, per 1000 atoms: 0.22 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: 0.33 Conformation dependent library (CDL) restraints added in 126.7 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: 0.09 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: 0.43 Time building geometry restraints manager: 0.35 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 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: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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= 0.299 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG A 38 TYR 0.023 0.004 TYR A 85 PHE 0.019 0.002 PHE A 202 TRP 0.007 0.001 TRP A 78 HIS 0.001 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.30 ( 4054) covalent geometry : angle 0.74910 / 0.44 ( 5534) hydrogen bonds : bond 0.07682 / 5.12 ( 314) hydrogen bonds : angle 5.11725 / 3.75 ( 924) *********************** 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 : 0.134 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: 0.0843 time to fit residues: 6.7386 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3959 r_free = 0.3959 target = 0.176720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115482 restraints weight = 3859.539| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.40 r_work: 0.3071 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4054 Z= 0.145 Angle : 0.526 5.043 5534 Z= 0.284 Chirality : 0.040 0.157 650 Planarity : 0.003 0.016 668 Dihedral : 5.486 50.324 818 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.39), residues: 480 helix: 1.92 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.76 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.015 0.001 TYR A 85 PHE 0.012 0.001 PHE A 109 TRP 0.002 0.000 TRP A 184 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4054) covalent geometry : angle 0.52558 / 0.28 ( 5534) hydrogen bonds : bond 0.03765 / 2.54 ( 314) hydrogen bonds : angle 3.71793 / 2.73 ( 924) *********************** 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 : 0.132 Fit side-chains REVERT: A 135 LEU cc_start: 0.6948 (tp) cc_final: 0.6336 (mp) REVERT: B 135 LEU cc_start: 0.6944 (tp) cc_final: 0.6333 (mp) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.0837 time to fit residues: 5.5122 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 5 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.175213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113084 restraints weight = 3853.572| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.33 r_work: 0.3046 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4054 Z= 0.166 Angle : 0.521 5.060 5534 Z= 0.278 Chirality : 0.040 0.148 650 Planarity : 0.003 0.018 668 Dihedral : 5.514 48.916 818 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.40), residues: 480 helix: 2.42 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.48 (0.83), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.012 0.001 TYR B 85 PHE 0.010 0.001 PHE A 109 TRP 0.001 0.000 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 4054) covalent geometry : angle 0.52096 / 0.28 ( 5534) hydrogen bonds : bond 0.03787 / 2.57 ( 314) hydrogen bonds : angle 3.55192 / 2.62 ( 924) *********************** 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 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.115 Fit side-chains REVERT: A 135 LEU cc_start: 0.7013 (tp) cc_final: 0.6404 (mp) REVERT: B 135 LEU cc_start: 0.7024 (tp) cc_final: 0.6418 (mp) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.0658 time to fit residues: 4.4232 Evaluate side-chains 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3956 r_free = 0.3956 target = 0.176928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113946 restraints weight = 3802.397| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.40 r_work: 0.3004 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2114 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= 0.132 Angle : 0.477 5.027 5534 Z= 0.253 Chirality : 0.038 0.139 650 Planarity : 0.002 0.017 668 Dihedral : 5.349 47.118 818 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.03 % Allowed : 6.96 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.40), residues: 480 helix: 2.68 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.69 (0.87), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.011 0.001 TYR B 85 PHE 0.010 0.001 PHE B 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4054) covalent geometry : angle 0.47681 / 0.25 ( 5534) hydrogen bonds : bond 0.03388 / 2.30 ( 314) hydrogen bonds : angle 3.36594 / 2.49 ( 924) *********************** 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 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.091 Fit side-chains REVERT: A 135 LEU cc_start: 0.7021 (tp) cc_final: 0.6409 (mp) REVERT: B 135 LEU cc_start: 0.7023 (tp) cc_final: 0.6422 (mp) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.0732 time to fit residues: 4.2817 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113946 restraints weight = 3807.422| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.39 r_work: 0.3028 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2244 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= 0.136 Angle : 0.481 5.101 5534 Z= 0.254 Chirality : 0.038 0.132 650 Planarity : 0.003 0.017 668 Dihedral : 5.323 44.820 818 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 6.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.40), residues: 480 helix: 2.85 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.62 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.009 0.001 TYR A 85 PHE 0.010 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4054) covalent geometry : angle 0.48070 / 0.25 ( 5534) hydrogen bonds : bond 0.03384 / 2.29 ( 314) hydrogen bonds : angle 3.34276 / 2.48 ( 924) *********************** 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 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.134 Fit side-chains REVERT: A 135 LEU cc_start: 0.6964 (tp) cc_final: 0.6387 (mp) REVERT: B 135 LEU cc_start: 0.6978 (tp) cc_final: 0.6404 (mp) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.0623 time to fit residues: 3.9873 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 22 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114079 restraints weight = 3905.853| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.41 r_work: 0.3006 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2310 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= 0.136 Angle : 0.486 5.107 5534 Z= 0.257 Chirality : 0.038 0.127 650 Planarity : 0.003 0.025 668 Dihedral : 5.246 42.581 818 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 7.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.40), residues: 480 helix: 2.95 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.63 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 137 TYR 0.009 0.001 TYR B 113 PHE 0.010 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4054) covalent geometry : angle 0.48580 / 0.26 ( 5534) hydrogen bonds : bond 0.03310 / 2.25 ( 314) hydrogen bonds : angle 3.27022 / 2.43 ( 924) *********************** 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 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.080 Fit side-chains REVERT: A 135 LEU cc_start: 0.6974 (tp) cc_final: 0.6397 (mp) REVERT: B 135 LEU cc_start: 0.6960 (tp) cc_final: 0.6392 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0665 time to fit residues: 4.1037 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 : 0.140 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116723 restraints weight = 3885.575| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.35 r_work: 0.3030 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2352 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= 0.142 Angle : 0.490 5.137 5534 Z= 0.258 Chirality : 0.039 0.162 650 Planarity : 0.003 0.026 668 Dihedral : 5.202 39.099 818 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.03 % Allowed : 7.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.40), residues: 480 helix: 3.01 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.73 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4054) covalent geometry : angle 0.48972 / 0.26 ( 5534) hydrogen bonds : bond 0.03349 / 2.27 ( 314) hydrogen bonds : angle 3.27855 / 2.43 ( 924) *********************** 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: 4 poor density : 50 time to evaluate : 0.192 Fit side-chains REVERT: A 135 LEU cc_start: 0.7047 (tp) cc_final: 0.6444 (mp) REVERT: B 135 LEU cc_start: 0.7044 (tp) cc_final: 0.6459 (mp) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.1107 time to fit residues: 7.0157 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 : 0.193 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.176214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113880 restraints weight = 3861.439| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.34 r_work: 0.3059 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4054 Z= 0.173 Angle : 0.513 5.212 5534 Z= 0.272 Chirality : 0.040 0.156 650 Planarity : 0.003 0.025 668 Dihedral : 5.312 39.077 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.55 % Allowed : 6.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.40), residues: 480 helix: 2.94 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.72 (0.84), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.010 0.001 TYR B 96 PHE 0.009 0.001 PHE B 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 4054) covalent geometry : angle 0.51326 / 0.27 ( 5534) hydrogen bonds : bond 0.03604 / 2.45 ( 314) hydrogen bonds : angle 3.35188 / 2.49 ( 924) *********************** 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 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.136 Fit side-chains REVERT: A 135 LEU cc_start: 0.7083 (tp) cc_final: 0.6447 (mp) REVERT: B 135 LEU cc_start: 0.7100 (tp) cc_final: 0.6457 (mp) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.0880 time to fit residues: 5.5870 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 : 0.133 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116587 restraints weight = 3920.594| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.37 r_work: 0.3056 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2445 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= 0.139 Angle : 0.543 11.350 5534 Z= 0.266 Chirality : 0.038 0.155 650 Planarity : 0.003 0.024 668 Dihedral : 5.165 38.573 818 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.13 (0.40), residues: 480 helix: 3.00 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.57 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE A 109 TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4054) covalent geometry : angle 0.54269 / 0.27 ( 5534) hydrogen bonds : bond 0.03298 / 2.23 ( 314) hydrogen bonds : angle 3.26264 / 2.42 ( 924) *********************** 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 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.149 Fit side-chains REVERT: A 135 LEU cc_start: 0.7080 (tp) cc_final: 0.6459 (mp) REVERT: B 135 LEU cc_start: 0.7067 (tp) cc_final: 0.6476 (mp) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.0875 time to fit residues: 5.5498 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 : 0.163 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124332 restraints weight = 3836.442| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.52 r_work: 0.3059 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2568 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= 0.127 Angle : 0.529 10.697 5534 Z= 0.259 Chirality : 0.038 0.158 650 Planarity : 0.003 0.023 668 Dihedral : 5.021 37.538 818 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 9.28 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.40), residues: 480 helix: 3.07 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.50 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE A 109 TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4054) covalent geometry : angle 0.52874 / 0.26 ( 5534) hydrogen bonds : bond 0.03146 / 2.13 ( 314) hydrogen bonds : angle 3.19968 / 2.37 ( 924) ********************** 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 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.136 Fit side-chains REVERT: A 135 LEU cc_start: 0.7057 (tp) cc_final: 0.6462 (mp) REVERT: B 135 LEU cc_start: 0.7070 (tp) cc_final: 0.6476 (mp) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.0869 time to fit residues: 5.5030 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 : 0.130 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119754 restraints weight = 3891.207| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.81 r_work: 0.3080 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2531 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= 0.143 Angle : 0.538 10.442 5534 Z= 0.266 Chirality : 0.039 0.154 650 Planarity : 0.003 0.023 668 Dihedral : 5.059 37.197 818 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 9.02 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.22 (0.40), residues: 480 helix: 3.05 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.59 (0.84), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.009 0.001 TYR A 96 PHE 0.009 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4054) covalent geometry : angle 0.53797 / 0.27 ( 5534) hydrogen bonds : bond 0.03301 / 2.24 ( 314) hydrogen bonds : angle 3.25063 / 2.41 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1011.18 seconds wall clock time: 17 minutes 58.15 seconds (1078.15 seconds total)