Starting phenix.real_space_refine on Wed Mar 5 15:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.map" model { file = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y13_33555/03_2025/7y13_33555.cif" } resolution = 3.1 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1479 2.51 5 N 342 2.21 5 O 356 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: 2199 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2071 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'PLM': 7} Classifications: {'undetermined': 7, 'water': 2} Link IDs: {None: 8} Time building chain proxies: 2.35, per 1000 atoms: 1.07 Number of scatterers: 2199 At special positions: 0 Unit cell: (56.7, 66.825, 68.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 356 8.00 N 342 7.00 C 1479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 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: 0.58 Conformation dependent library (CDL) restraints added in 252.7 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 removed outlier: 3.575A pdb=" N LEU R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 86 removed outlier: 3.750A pdb=" N ILE R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 129 removed outlier: 3.538A pdb=" N LEU R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 172 through 209 removed outlier: 3.512A pdb=" N PHE R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG R 177 " --> pdb=" O ASP R 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 216 through 245 removed outlier: 4.240A pdb=" N LEU R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) Proline residue: R 236 - end of helix removed outlier: 3.800A pdb=" N TRP R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix 166 hydrogen bonds defined for protein. 498 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: 0.53 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 629 1.35 - 1.46: 570 1.46 - 1.58: 1014 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 2246 Sorted by residual: bond pdb=" C2 PLM R 407 " pdb=" C3 PLM R 407 " ideal model delta sigma weight residual 1.522 1.493 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C2 PLM R 405 " pdb=" C3 PLM R 405 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C2 PLM R 403 " pdb=" C3 PLM R 403 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C2 PLM R 406 " pdb=" C3 PLM R 406 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C2 PLM R 401 " pdb=" C3 PLM R 401 " ideal model delta sigma weight residual 1.522 1.497 0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 2241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 2912 1.66 - 3.32: 90 3.32 - 4.98: 14 4.98 - 6.64: 2 6.64 - 8.30: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" CA LEU R 52 " pdb=" CB LEU R 52 " pdb=" CG LEU R 52 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 angle pdb=" C LYS R 166 " pdb=" N PHE R 167 " pdb=" CA PHE R 167 " ideal model delta sigma weight residual 120.17 123.62 -3.45 1.54e+00 4.22e-01 5.01e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.38 3.76 1.75e+00 3.27e-01 4.62e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 117.63 -4.03 1.90e+00 2.77e-01 4.49e+00 angle pdb=" N PHE R 167 " pdb=" CA PHE R 167 " pdb=" C PHE R 167 " ideal model delta sigma weight residual 113.50 110.22 3.28 1.65e+00 3.67e-01 3.94e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1117 11.54 - 23.08: 142 23.08 - 34.63: 59 34.63 - 46.17: 23 46.17 - 57.71: 4 Dihedral angle restraints: 1345 sinusoidal: 563 harmonic: 782 Sorted by residual: dihedral pdb=" CG ARG R 103 " pdb=" CD ARG R 103 " pdb=" NE ARG R 103 " pdb=" CZ ARG R 103 " ideal model delta sinusoidal sigma weight residual -90.00 -134.56 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA HIS R 57 " pdb=" C HIS R 57 " pdb=" N ARG R 58 " pdb=" CA ARG R 58 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB MET R 35 " pdb=" CG MET R 35 " pdb=" SD MET R 35 " pdb=" CE MET R 35 " ideal model delta sinusoidal sigma weight residual 60.00 117.71 -57.71 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 219 0.031 - 0.062: 103 0.062 - 0.092: 20 0.092 - 0.123: 8 0.123 - 0.154: 1 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO R 236 " pdb=" N PRO R 236 " pdb=" C PRO R 236 " pdb=" CB PRO R 236 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 348 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 235 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO R 236 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP R 144 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 187 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C MET R 187 " 0.030 2.00e-02 2.50e+03 pdb=" O MET R 187 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 188 " -0.010 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 134 2.74 - 3.28: 2109 3.28 - 3.82: 3736 3.82 - 4.36: 4123 4.36 - 4.90: 7542 Nonbonded interactions: 17644 Sorted by model distance: nonbonded pdb=" NH2 ARG R 137 " pdb=" OG SER R 142 " model vdw 2.195 3.120 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.211 3.040 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.411 3.120 nonbonded pdb=" OG1 THR R 22 " pdb=" N VAL R 23 " model vdw 2.435 3.120 nonbonded pdb=" O SER R 78 " pdb=" OG SER R 81 " model vdw 2.436 3.040 ... (remaining 17639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.320 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.880 Find NCS groups from input model: 0.020 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2246 Z= 0.321 Angle : 0.676 8.296 3019 Z= 0.339 Chirality : 0.038 0.154 351 Planarity : 0.005 0.075 350 Dihedral : 13.192 57.709 830 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.88 (0.56), residues: 262 helix: 1.91 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.24 (0.94), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 144 HIS 0.001 0.000 HIS R 57 PHE 0.014 0.001 PHE R 202 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1263 time to fit residues: 5.2229 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 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 = 0.3997 r_free = 0.3997 target = 0.181354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139755 restraints weight = 2159.088| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.81 r_work: 0.3254 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2246 Z= 0.238 Angle : 0.603 7.754 3019 Z= 0.302 Chirality : 0.038 0.177 351 Planarity : 0.005 0.075 350 Dihedral : 8.785 47.706 382 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.43 % Allowed : 8.62 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.56), residues: 262 helix: 1.93 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.02 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 144 HIS 0.005 0.001 HIS R 57 PHE 0.016 0.002 PHE R 202 TYR 0.006 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.223 Fit side-chains REVERT: R 95 ASP cc_start: 0.7369 (t0) cc_final: 0.6994 (t0) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1081 time to fit residues: 4.6483 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139850 restraints weight = 2150.927| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.83 r_work: 0.3236 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2246 Z= 0.227 Angle : 0.573 7.106 3019 Z= 0.291 Chirality : 0.038 0.172 351 Planarity : 0.005 0.075 350 Dihedral : 9.058 50.057 382 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.86 % Allowed : 12.07 % Favored : 87.07 % 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: 2.20 (0.56), residues: 262 helix: 2.04 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -0.91 (1.02), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.015 0.001 PHE R 202 TYR 0.006 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.228 Fit side-chains REVERT: R 185 LEU cc_start: 0.7937 (tt) cc_final: 0.7475 (tp) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.1067 time to fit residues: 5.1343 Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.184374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142334 restraints weight = 2105.975| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.85 r_work: 0.3258 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2246 Z= 0.161 Angle : 0.545 10.418 3019 Z= 0.273 Chirality : 0.036 0.156 351 Planarity : 0.005 0.074 350 Dihedral : 8.932 49.761 382 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.86 % Allowed : 14.66 % Favored : 84.48 % 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: 2.54 (0.57), residues: 262 helix: 2.42 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.19 (0.96), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.003 0.000 HIS R 57 PHE 0.013 0.001 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.213 Fit side-chains REVERT: R 185 LEU cc_start: 0.7896 (tt) cc_final: 0.7447 (tp) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1044 time to fit residues: 4.5049 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.182724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140636 restraints weight = 2163.118| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2246 Z= 0.190 Angle : 0.565 10.748 3019 Z= 0.282 Chirality : 0.037 0.161 351 Planarity : 0.005 0.074 350 Dihedral : 9.376 56.860 382 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.86 % Allowed : 15.52 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.57), residues: 262 helix: 2.52 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.12 (0.98), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.014 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.266 Fit side-chains REVERT: R 185 LEU cc_start: 0.7924 (tt) cc_final: 0.7485 (tp) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1171 time to fit residues: 4.7670 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140127 restraints weight = 2163.165| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.85 r_work: 0.3236 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2246 Z= 0.204 Angle : 0.571 10.495 3019 Z= 0.285 Chirality : 0.037 0.166 351 Planarity : 0.005 0.075 350 Dihedral : 9.816 58.176 382 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.86 % Allowed : 16.81 % Favored : 82.33 % 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: 2.74 (0.57), residues: 262 helix: 2.54 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.05 (0.98), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.015 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.269 Fit side-chains REVERT: R 185 LEU cc_start: 0.7957 (tt) cc_final: 0.7533 (tp) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1059 time to fit residues: 4.3226 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.183515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141095 restraints weight = 2168.668| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.88 r_work: 0.3242 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2246 Z= 0.163 Angle : 0.542 10.287 3019 Z= 0.272 Chirality : 0.036 0.156 351 Planarity : 0.005 0.073 350 Dihedral : 9.620 58.139 382 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.29 % Allowed : 17.67 % Favored : 81.03 % 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: 2.87 (0.57), residues: 262 helix: 2.67 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.16 (0.97), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.019 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.203 Fit side-chains REVERT: R 185 LEU cc_start: 0.7947 (tt) cc_final: 0.7501 (tp) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.1073 time to fit residues: 4.8502 Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 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 = 0.3992 r_free = 0.3992 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139670 restraints weight = 2181.875| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.84 r_work: 0.3227 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2246 Z= 0.218 Angle : 0.581 10.693 3019 Z= 0.291 Chirality : 0.038 0.169 351 Planarity : 0.005 0.074 350 Dihedral : 9.914 57.889 382 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.86 % Allowed : 17.67 % Favored : 81.47 % 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: 2.82 (0.56), residues: 262 helix: 2.48 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -0.75 (1.04), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.019 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.229 Fit side-chains REVERT: R 185 LEU cc_start: 0.7968 (tt) cc_final: 0.7551 (tp) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.0951 time to fit residues: 4.0320 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.181011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139460 restraints weight = 2163.730| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.84 r_work: 0.3222 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2246 Z= 0.220 Angle : 0.581 10.622 3019 Z= 0.291 Chirality : 0.038 0.168 351 Planarity : 0.005 0.074 350 Dihedral : 9.979 58.601 382 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.29 % Allowed : 17.67 % Favored : 81.03 % 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: 2.80 (0.56), residues: 262 helix: 2.55 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.99 (1.02), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.020 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.178 Fit side-chains REVERT: R 185 LEU cc_start: 0.7961 (tt) cc_final: 0.7552 (tp) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1076 time to fit residues: 4.5077 Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.182501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140513 restraints weight = 2130.617| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.85 r_work: 0.3240 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2246 Z= 0.178 Angle : 0.557 10.591 3019 Z= 0.280 Chirality : 0.037 0.157 351 Planarity : 0.005 0.074 350 Dihedral : 9.702 58.752 382 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.43 % Allowed : 18.97 % Favored : 80.60 % 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: 3.00 (0.56), residues: 262 helix: 2.62 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -0.77 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.024 0.002 PHE R 75 TYR 0.007 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.224 Fit side-chains REVERT: R 185 LEU cc_start: 0.7929 (tt) cc_final: 0.7492 (tp) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.1118 time to fit residues: 4.2568 Evaluate side-chains 29 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.180897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139576 restraints weight = 2144.198| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.82 r_work: 0.3230 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2246 Z= 0.222 Angle : 0.586 11.063 3019 Z= 0.294 Chirality : 0.038 0.170 351 Planarity : 0.005 0.075 350 Dihedral : 10.050 59.255 382 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.43 % Allowed : 18.97 % Favored : 80.60 % 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: 2.88 (0.56), residues: 262 helix: 2.60 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -0.95 (1.02), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.002 0.000 HIS R 57 PHE 0.023 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.74 seconds wall clock time: 25 minutes 11.73 seconds (1511.73 seconds total)