Starting phenix.real_space_refine on Wed Jul 23 08:10:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y13_33555/07_2025/7y13_33555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y13_33555/07_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_33555/07_2025/7y13_33555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y13_33555/07_2025/7y13_33555.map" model { file = "/net/cci-nas-00/data/ceres_data/7y13_33555/07_2025/7y13_33555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y13_33555/07_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-5711/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: 3.35, per 1000 atoms: 1.52 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: 0.62 Conformation dependent library (CDL) restraints added in 280.3 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: 0.15 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: 0.60 Time building geometry restraints manager: 0.74 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: 2.300 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.690 Find NCS groups from input model: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- 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 2247 Z= 0.240 Angle : 0.677 8.296 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.09114 ( 166) hydrogen bonds : angle 6.38148 ( 498) SS BOND : bond 0.00430 ( 1) SS BOND : angle 1.21361 ( 2) covalent geometry : bond 0.00501 ( 2246) covalent geometry : angle 0.67624 ( 3019) *********************** 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 : 0.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1125 time to fit residues: 4.6410 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 : 0.211 ------------------------------------------------------------------------------- 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 2247 Z= 0.164 Angle : 0.604 7.754 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 166) hydrogen bonds : angle 5.05774 ( 498) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.22961 ( 2) covalent geometry : bond 0.00395 ( 2246) covalent geometry : angle 0.60343 ( 3019) *********************** 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 : 0.288 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: 0.1456 time to fit residues: 6.2528 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 : 0.263 ------------------------------------------------------------------------------- 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 2247 Z= 0.156 Angle : 0.573 7.106 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 166) hydrogen bonds : angle 4.94888 ( 498) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.90696 ( 2) covalent geometry : bond 0.00374 ( 2246) covalent geometry : angle 0.57288 ( 3019) *********************** 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 : 0.231 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: 0.1206 time to fit residues: 5.7378 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 : 0.234 ------------------------------------------------------------------------------- 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 2247 Z= 0.116 Angle : 0.546 10.418 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 166) hydrogen bonds : angle 4.73143 ( 498) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.83423 ( 2) covalent geometry : bond 0.00263 ( 2246) covalent geometry : angle 0.54538 ( 3019) *********************** 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 : 0.217 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: 0.1088 time to fit residues: 4.7309 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 : 0.233 ------------------------------------------------------------------------------- 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 2247 Z= 0.133 Angle : 0.565 10.748 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 166) hydrogen bonds : angle 4.74893 ( 498) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.94414 ( 2) covalent geometry : bond 0.00310 ( 2246) covalent geometry : angle 0.56513 ( 3019) *********************** 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 : 0.241 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: 0.1138 time to fit residues: 4.6180 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 : 0.229 ------------------------------------------------------------------------------- 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 2247 Z= 0.141 Angle : 0.571 10.495 3021 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 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 166) hydrogen bonds : angle 4.77040 ( 498) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.02791 ( 2) covalent geometry : bond 0.00334 ( 2246) covalent geometry : angle 0.57082 ( 3019) *********************** 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 : 0.222 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: 0.1112 time to fit residues: 4.5510 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.3980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.183410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140954 restraints weight = 2168.948| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.88 r_work: 0.3243 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2247 Z= 0.121 Angle : 0.545 10.271 3021 Z= 0.273 Chirality : 0.036 0.157 351 Planarity : 0.005 0.074 350 Dihedral : 9.635 57.017 382 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.79 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: 2.84 (0.57), residues: 262 helix: 2.65 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -1.15 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 166) hydrogen bonds : angle 4.67376 ( 498) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.92902 ( 2) covalent geometry : bond 0.00277 ( 2246) covalent geometry : angle 0.54446 ( 3019) *********************** 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 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: R 185 LEU cc_start: 0.7937 (tt) cc_final: 0.7487 (tp) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.1106 time to fit residues: 4.7616 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 : 0.232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.182131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140368 restraints weight = 2177.697| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.85 r_work: 0.3232 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2247 Z= 0.139 Angle : 0.569 10.637 3021 Z= 0.285 Chirality : 0.037 0.165 351 Planarity : 0.005 0.074 350 Dihedral : 9.779 57.973 382 Min Nonbonded Distance : 2.626 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: 2.76 (0.56), residues: 262 helix: 2.58 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -1.14 (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 0.019 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 166) hydrogen bonds : angle 4.73017 ( 498) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.98756 ( 2) covalent geometry : bond 0.00329 ( 2246) covalent geometry : angle 0.56899 ( 3019) *********************** 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 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.231 Fit side-chains REVERT: R 185 LEU cc_start: 0.7961 (tt) cc_final: 0.7536 (tp) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1122 time to fit residues: 4.5493 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 : 0.211 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.0070 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.182514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140989 restraints weight = 2151.461| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.83 r_work: 0.3239 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2247 Z= 0.131 Angle : 0.559 10.575 3021 Z= 0.280 Chirality : 0.037 0.161 351 Planarity : 0.005 0.074 350 Dihedral : 9.676 58.442 382 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.29 % Allowed : 16.81 % Favored : 81.90 % 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: 2.89 (0.56), residues: 262 helix: 2.70 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -1.08 (0.96), residues: 59 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 0.018 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 166) hydrogen bonds : angle 4.69000 ( 498) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.88574 ( 2) covalent geometry : bond 0.00307 ( 2246) covalent geometry : angle 0.55893 ( 3019) *********************** 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 : 0.237 Fit side-chains REVERT: R 57 HIS cc_start: 0.4973 (OUTLIER) cc_final: 0.3288 (p-80) REVERT: R 185 LEU cc_start: 0.7960 (tt) cc_final: 0.7524 (tp) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1305 time to fit residues: 5.5546 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 57 HIS 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: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.182806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140566 restraints weight = 2127.737| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.86 r_work: 0.3232 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2247 Z= 0.128 Angle : 0.557 10.553 3021 Z= 0.279 Chirality : 0.037 0.160 351 Planarity : 0.005 0.074 350 Dihedral : 9.632 58.858 382 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.29 % Allowed : 17.24 % 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: 2.92 (0.56), residues: 262 helix: 2.74 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -1.10 (0.96), residues: 59 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 0.018 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 166) hydrogen bonds : angle 4.66478 ( 498) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.88985 ( 2) covalent geometry : bond 0.00300 ( 2246) covalent geometry : angle 0.55626 ( 3019) ********************** 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 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.248 Fit side-chains REVERT: R 57 HIS cc_start: 0.4977 (OUTLIER) cc_final: 0.3313 (p-80) REVERT: R 185 LEU cc_start: 0.7958 (tt) cc_final: 0.7516 (tp) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.1230 time to fit residues: 5.2618 Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 57 HIS 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 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139596 restraints weight = 2140.624| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.82 r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2247 Z= 0.150 Angle : 0.577 10.544 3021 Z= 0.290 Chirality : 0.038 0.170 351 Planarity : 0.005 0.075 350 Dihedral : 9.988 59.252 382 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.68 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: 2.94 (0.56), residues: 262 helix: 2.66 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -0.88 (1.00), 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 0.017 0.002 PHE R 75 TYR 0.006 0.001 TYR R 109 ARG 0.001 0.000 ARG R 262 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 166) hydrogen bonds : angle 4.73805 ( 498) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.85014 ( 2) covalent geometry : bond 0.00358 ( 2246) covalent geometry : angle 0.57702 ( 3019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.67 seconds wall clock time: 27 minutes 10.14 seconds (1630.14 seconds total)