Starting phenix.real_space_refine on Fri Dec 27 04:49:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.map" model { file = "/net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y14_33556/12_2024/7y14_33556.cif" } resolution = 3.2 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= -0.003 sd= 0.055 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 1431 2.51 5 N 342 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2145 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2073 Unusual residues: {'BAL': 1} Classifications: {'peptide': 264, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PRE-BETA-TRANS': 1, 'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PLM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.78, per 1000 atoms: 1.30 Number of scatterers: 2145 At special positions: 0 Unit cell: (57.375, 68.175, 69.525, 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 350 8.00 N 342 7.00 C 1431 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: 0.71 Conformation dependent library (CDL) restraints added in 276.8 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 22 through 52 removed outlier: 3.709A pdb=" N LEU R 28 " --> pdb=" O HIS R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 86 Processing helix chain 'R' and resid 95 through 129 removed outlier: 3.733A 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 189 Processing helix chain 'R' and resid 189 through 209 Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 242 removed outlier: 4.188A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix 171 hydrogen bonds defined for protein. 513 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: 0.58 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 427 1.33 - 1.45: 506 1.45 - 1.57: 1230 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 2196 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.566 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA BAL R1001 " pdb=" C BAL R1001 " ideal model delta sigma weight residual 1.525 1.500 0.025 2.10e-02 2.27e+03 1.40e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.565 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 2836 1.49 - 2.98: 113 2.98 - 4.47: 12 4.47 - 5.96: 5 5.96 - 7.46: 3 Bond angle restraints: 2969 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.34 7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.23e+00 angle pdb=" N MET R 79 " pdb=" CA MET R 79 " pdb=" CB MET R 79 " ideal model delta sigma weight residual 110.16 113.87 -3.71 1.48e+00 4.57e-01 6.30e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 118.12 -4.52 1.90e+00 2.77e-01 5.65e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.15 3.99 1.75e+00 3.27e-01 5.19e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1146 16.25 - 32.51: 131 32.51 - 48.76: 20 48.76 - 65.01: 3 65.01 - 81.27: 1 Dihedral angle restraints: 1301 sinusoidal: 519 harmonic: 782 Sorted by residual: dihedral pdb=" CB GLU R 99 " pdb=" CG GLU R 99 " pdb=" CD GLU R 99 " pdb=" OE1 GLU R 99 " ideal model delta sinusoidal sigma weight residual 0.00 81.27 -81.27 1 3.00e+01 1.11e-03 9.05e+00 dihedral pdb=" CB MET R 180 " pdb=" CG MET R 180 " pdb=" SD MET R 180 " pdb=" CE MET R 180 " ideal model delta sinusoidal sigma weight residual 60.00 110.60 -50.60 3 1.50e+01 4.44e-03 8.92e+00 dihedral pdb=" CA LEU R 228 " pdb=" CB LEU R 228 " pdb=" CG LEU R 228 " pdb=" CD1 LEU R 228 " ideal model delta sinusoidal sigma weight residual 180.00 134.54 45.46 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 224 0.031 - 0.063: 95 0.063 - 0.094: 22 0.094 - 0.125: 5 0.125 - 0.157: 5 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 2.35 0.16 2.00e-01 2.50e+01 6.13e-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 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA THR R 191 " pdb=" N THR R 191 " pdb=" C THR R 191 " pdb=" CB THR R 191 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 348 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.020 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" CG TRP R 144 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.001 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 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 88 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 89 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R 215 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO R 216 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 631 2.83 - 3.35: 2146 3.35 - 3.86: 3635 3.86 - 4.38: 3981 4.38 - 4.90: 7063 Nonbonded interactions: 17456 Sorted by model distance: nonbonded pdb=" OD2 ASP R 179 " pdb=" N BAL R1001 " model vdw 2.312 3.120 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.332 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.460 3.040 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.461 3.120 nonbonded pdb=" O GLY R 41 " pdb=" ND2 ASN R 45 " model vdw 2.471 3.120 ... (remaining 17451 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.400 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2196 Z= 0.258 Angle : 0.663 7.456 2969 Z= 0.351 Chirality : 0.039 0.157 351 Planarity : 0.005 0.059 348 Dihedral : 13.603 81.268 786 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.56), residues: 262 helix: 2.33 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.20 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.002 PHE R 75 TYR 0.012 0.002 TYR R 106 ARG 0.003 0.000 ARG R 214 *********************** 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 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1135 time to fit residues: 5.4455 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2196 Z= 0.181 Angle : 0.544 6.552 2969 Z= 0.277 Chirality : 0.037 0.153 351 Planarity : 0.005 0.056 348 Dihedral : 7.554 59.172 342 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.43 % Allowed : 5.19 % Favored : 94.37 % Cbeta Deviations : 0.39 % 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 (0.55), residues: 262 helix: 2.62 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.19 (1.01), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.019 0.002 PHE R 75 TYR 0.016 0.002 TYR R 245 ARG 0.002 0.000 ARG R 103 *********************** 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 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.212 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1033 time to fit residues: 4.3869 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 : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2196 Z= 0.194 Angle : 0.536 6.498 2969 Z= 0.272 Chirality : 0.038 0.153 351 Planarity : 0.005 0.053 348 Dihedral : 7.583 58.749 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.30 % Allowed : 9.09 % Favored : 89.61 % Cbeta Deviations : 0.39 % 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: 3.05 (0.56), residues: 262 helix: 2.70 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.08 (1.06), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.016 0.002 PHE R 75 TYR 0.016 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.240 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.1216 time to fit residues: 4.8002 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2196 Z= 0.183 Angle : 0.519 6.374 2969 Z= 0.266 Chirality : 0.037 0.151 351 Planarity : 0.005 0.051 348 Dihedral : 7.477 59.031 342 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 11.69 % Favored : 87.45 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.56), residues: 262 helix: 2.80 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.06 (1.05), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.016 0.001 PHE R 75 TYR 0.017 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.332 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.1084 time to fit residues: 4.3555 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.0010 chunk 6 optimal weight: 0.0070 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2196 Z= 0.129 Angle : 0.500 6.234 2969 Z= 0.251 Chirality : 0.035 0.149 351 Planarity : 0.005 0.049 348 Dihedral : 6.864 56.026 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.43 % Allowed : 14.72 % Favored : 84.85 % Cbeta Deviations : 0.39 % 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: 3.41 (0.55), residues: 262 helix: 3.02 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.21 (1.00), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.013 0.001 PHE R 75 TYR 0.018 0.002 TYR R 245 ARG 0.002 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 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1042 time to fit residues: 4.5449 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2196 Z= 0.200 Angle : 0.532 6.476 2969 Z= 0.272 Chirality : 0.038 0.151 351 Planarity : 0.005 0.048 348 Dihedral : 7.355 57.589 342 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 16.88 % Favored : 82.25 % Cbeta Deviations : 0.39 % 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: 3.26 (0.55), residues: 262 helix: 2.89 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.21 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 144 HIS 0.003 0.001 HIS R 98 PHE 0.019 0.002 PHE R 75 TYR 0.018 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.249 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1179 time to fit residues: 5.0554 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.0060 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2196 Z= 0.140 Angle : 0.490 5.504 2969 Z= 0.252 Chirality : 0.036 0.135 351 Planarity : 0.005 0.047 348 Dihedral : 6.935 56.636 342 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % Cbeta Deviations : 0.39 % 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: 3.37 (0.55), residues: 262 helix: 3.01 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.33 (0.99), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.020 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 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 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1026 time to fit residues: 4.3795 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2196 Z= 0.147 Angle : 0.495 5.401 2969 Z= 0.255 Chirality : 0.036 0.137 351 Planarity : 0.005 0.047 348 Dihedral : 6.893 57.435 342 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.87 % Allowed : 19.48 % Favored : 79.65 % Cbeta Deviations : 0.39 % 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: 3.43 (0.55), residues: 262 helix: 3.05 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -1.31 (1.00), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 144 HIS 0.002 0.000 HIS R 98 PHE 0.019 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 : 0.241 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.0989 time to fit residues: 4.2314 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2196 Z= 0.140 Angle : 0.495 5.353 2969 Z= 0.255 Chirality : 0.035 0.135 351 Planarity : 0.005 0.046 348 Dihedral : 6.745 56.109 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.87 % Allowed : 19.48 % Favored : 79.65 % Cbeta Deviations : 0.39 % 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: 3.51 (0.55), residues: 262 helix: 3.12 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -1.33 (0.99), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.002 0.000 HIS R 98 PHE 0.021 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.001 0.000 ARG R 214 *********************** 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 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.207 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.0893 time to fit residues: 3.8678 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.191 Angle : 0.539 5.735 2969 Z= 0.277 Chirality : 0.037 0.147 351 Planarity : 0.005 0.046 348 Dihedral : 7.143 57.107 342 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.87 % Allowed : 19.05 % Favored : 80.09 % Cbeta Deviations : 0.39 % 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: 3.34 (0.55), residues: 262 helix: 2.95 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.22 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.025 0.002 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 ********************** 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 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.226 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.0857 time to fit residues: 3.6838 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.157635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131442 restraints weight = 2480.388| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.73 r_work: 0.3360 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 0.023 2196 Z= 0.194 Angle : 0.555 7.871 2969 Z= 0.287 Chirality : 0.038 0.147 351 Planarity : 0.005 0.046 348 Dihedral : 7.179 57.191 342 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.87 % Allowed : 19.91 % Favored : 79.22 % Cbeta Deviations : 0.39 % 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: 3.30 (0.55), residues: 262 helix: 2.98 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.37 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.029 0.002 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1035.77 seconds wall clock time: 19 minutes 43.93 seconds (1183.93 seconds total)