Starting phenix.real_space_refine on Mon Feb 10 20:28:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y14_33556/02_2025/7y14_33556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y14_33556/02_2025/7y14_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_33556/02_2025/7y14_33556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y14_33556/02_2025/7y14_33556.map" model { file = "/net/cci-nas-00/data/ceres_data/7y14_33556/02_2025/7y14_33556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y14_33556/02_2025/7y14_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-5592/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: 2.21, per 1000 atoms: 1.03 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: 0.64 Conformation dependent library (CDL) restraints added in 239.8 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: 0.20 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: 0.53 Time building geometry restraints manager: 0.69 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: 1.370 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.450 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- 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 : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1126 time to fit residues: 5.2412 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 : 0.236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137173 restraints weight = 2516.537| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.74 r_work: 0.3370 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.211 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0946 time to fit residues: 4.0340 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 : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.156660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131220 restraints weight = 2556.759| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.75 r_work: 0.3338 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0940 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= 0.200 Angle : 0.543 6.553 2969 Z= 0.275 Chirality : 0.038 0.154 351 Planarity : 0.005 0.053 348 Dihedral : 7.611 58.011 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.30 % Allowed : 8.66 % Favored : 90.04 % 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 0.028 0.002 TRP R 144 HIS 0.002 0.001 HIS R 140 PHE 0.015 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 : 0.232 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.1007 time to fit residues: 4.0603 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 : 0.221 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 0 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.158867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133200 restraints weight = 2462.520| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.74 r_work: 0.3378 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2196 Z= 0.145 Angle : 0.495 6.419 2969 Z= 0.252 Chirality : 0.036 0.153 351 Planarity : 0.005 0.050 348 Dihedral : 7.158 56.921 342 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.87 % Allowed : 12.99 % Favored : 86.15 % 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: 3.31 (0.55), residues: 262 helix: 2.97 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.25 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 144 HIS 0.002 0.000 HIS R 98 PHE 0.016 0.001 PHE R 75 TYR 0.017 0.002 TYR R 245 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 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 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.1090 time to fit residues: 4.6012 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.158006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132140 restraints weight = 2486.789| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.73 r_work: 0.3358 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1115 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= 0.162 Angle : 0.514 6.443 2969 Z= 0.261 Chirality : 0.037 0.153 351 Planarity : 0.005 0.049 348 Dihedral : 7.219 58.527 342 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % 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: 3.32 (0.55), residues: 262 helix: 2.98 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.30 (1.00), residues: 53 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 0.015 0.001 PHE R 75 TYR 0.017 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1035 time to fit residues: 4.2656 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.157321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131723 restraints weight = 2514.798| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.73 r_work: 0.3346 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1150 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= 0.206 Angle : 0.535 6.502 2969 Z= 0.273 Chirality : 0.038 0.153 351 Planarity : 0.005 0.048 348 Dihedral : 7.452 55.776 342 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 17.75 % Favored : 81.39 % 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: 3.23 (0.55), residues: 262 helix: 2.84 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.10 (1.05), 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 0.019 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 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.197 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.1076 time to fit residues: 4.5572 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 12 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 = 0.3790 r_free = 0.3790 target = 0.155856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129955 restraints weight = 2540.002| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.73 r_work: 0.3346 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1219 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= 0.186 Angle : 0.519 5.509 2969 Z= 0.267 Chirality : 0.037 0.146 351 Planarity : 0.005 0.047 348 Dihedral : 7.355 57.098 342 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 18.61 % 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: 3.25 (0.55), residues: 262 helix: 2.87 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.19 (1.03), residues: 51 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 0.020 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** 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 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.247 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1046 time to fit residues: 4.2213 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.159438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133395 restraints weight = 2512.187| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.75 r_work: 0.3372 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1297 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= 0.143 Angle : 0.518 7.864 2969 Z= 0.262 Chirality : 0.036 0.135 351 Planarity : 0.005 0.047 348 Dihedral : 7.087 58.210 342 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: 3.36 (0.55), residues: 262 helix: 3.03 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.38 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.001 0.000 HIS R 140 PHE 0.020 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.213 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.0954 time to fit residues: 4.2281 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 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 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.157855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131687 restraints weight = 2516.902| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.75 r_work: 0.3364 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2196 Z= 0.171 Angle : 0.544 7.952 2969 Z= 0.275 Chirality : 0.037 0.141 351 Planarity : 0.005 0.046 348 Dihedral : 7.182 59.465 342 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 3.37 (0.55), residues: 262 helix: 3.03 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.36 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.021 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 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 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.212 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.0982 time to fit residues: 4.2184 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 : 0.232 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.156855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130800 restraints weight = 2513.635| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.74 r_work: 0.3359 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2196 Z= 0.171 Angle : 0.519 5.385 2969 Z= 0.269 Chirality : 0.037 0.143 351 Planarity : 0.005 0.046 348 Dihedral : 7.173 58.608 342 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.30 % Allowed : 18.61 % 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: 3.36 (0.55), residues: 262 helix: 3.02 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.33 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.001 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 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.276 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1022 time to fit residues: 4.4078 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 : 0.236 ------------------------------------------------------------------------------- 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 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133393 restraints weight = 2500.292| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.75 r_work: 0.3362 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2196 Z= 0.169 Angle : 0.521 5.372 2969 Z= 0.272 Chirality : 0.037 0.142 351 Planarity : 0.005 0.046 348 Dihedral : 7.134 58.757 342 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.30 % Allowed : 19.05 % 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: 3.31 (0.55), residues: 262 helix: 2.98 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.34 (1.00), residues: 53 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 0.027 0.001 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: 1586.73 seconds wall clock time: 28 minutes 45.27 seconds (1725.27 seconds total)