Starting phenix.real_space_refine on Wed Mar 5 14:44:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggz_40026/03_2025/8ggz_40026.cif" } resolution = 3.9 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= 0.000 sd= 0.017 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 9 5.16 5 C 1324 2.51 5 N 327 2.21 5 O 334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1994 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1979 Classifications: {'peptide': 281} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 90} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 124 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 1.30 Number of scatterers: 1994 At special positions: 0 Unit cell: (56.4005, 85.0346, 61.6067, 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 9 16.00 O 334 8.00 N 327 7.00 C 1324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 293.4 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 536 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.941A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.307A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.938A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.602A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 297 removed outlier: 4.013A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.934A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 316 Processing helix chain 'R' and resid 317 through 320 Processing helix chain 'R' and resid 321 through 326 Processing helix chain 'R' and resid 329 through 338 162 hydrogen bonds defined for protein. 483 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: 0.57 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 615 1.34 - 1.46: 532 1.46 - 1.58: 889 1.58 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2049 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.542 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 2044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2674 1.12 - 2.24: 111 2.24 - 3.36: 24 3.36 - 4.48: 5 4.48 - 5.60: 6 Bond angle restraints: 2820 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.60e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 123.05 126.25 -3.20 1.57e+00 4.06e-01 4.16e+00 angle pdb=" C TRP R 173 " pdb=" N TYR R 174 " pdb=" CA TYR R 174 " ideal model delta sigma weight residual 123.91 127.07 -3.16 1.66e+00 3.63e-01 3.63e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.10 -5.47 3.00e+00 1.11e-01 3.32e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.29 117.75 2.54 1.42e+00 4.96e-01 3.19e+00 ... (remaining 2815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 1044 15.45 - 30.90: 80 30.90 - 46.35: 23 46.35 - 61.79: 1 61.79 - 77.24: 2 Dihedral angle restraints: 1150 sinusoidal: 324 harmonic: 826 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG R 131 " pdb=" CB ARG R 131 " pdb=" CG ARG R 131 " pdb=" CD ARG R 131 " ideal model delta sinusoidal sigma weight residual -180.00 -128.30 -51.70 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA MET R 82 " pdb=" CB MET R 82 " pdb=" CG MET R 82 " pdb=" SD MET R 82 " ideal model delta sinusoidal sigma weight residual 180.00 -134.27 -45.73 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 1147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 235 0.036 - 0.072: 87 0.072 - 0.108: 14 0.108 - 0.143: 1 0.143 - 0.179: 1 Chirality restraints: 338 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.58 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA TYR R 174 " pdb=" N TYR R 174 " pdb=" C TYR R 174 " pdb=" CB TYR R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.04e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.75e-01 ... (remaining 335 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO R 138 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 108 " 0.009 2.00e-02 2.50e+03 8.48e-03 1.26e+00 pdb=" CG PHE R 108 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 108 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 173 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C TRP R 173 " -0.018 2.00e-02 2.50e+03 pdb=" O TRP R 173 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR R 174 " 0.006 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 512 2.80 - 3.33: 2010 3.33 - 3.85: 3195 3.85 - 4.38: 2923 4.38 - 4.90: 5562 Nonbonded interactions: 14202 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.278 3.040 nonbonded pdb=" O LEU R 324 " pdb=" NH1 ARG R 328 " model vdw 2.366 3.120 nonbonded pdb=" OD1 ASP R 192 " pdb=" N PHE R 193 " model vdw 2.386 3.120 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.529 3.120 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.633 2.496 ... (remaining 14197 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 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: 11.520 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:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 0.055 2049 Z= 0.221 Angle : 0.580 5.601 2820 Z= 0.326 Chirality : 0.038 0.179 338 Planarity : 0.004 0.055 350 Dihedral : 12.741 77.243 614 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.53), residues: 277 helix: 2.79 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.26 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.019 0.001 PHE R 108 TYR 0.010 0.001 TYR R 219 ARG 0.002 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.202 Fit side-chains REVERT: R 131 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7616 (mtp85) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1090 time to fit residues: 6.5202 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.150183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135606 restraints weight = 3627.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138533 restraints weight = 1858.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140608 restraints weight = 1140.612| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2049 Z= 0.142 Angle : 0.483 4.740 2820 Z= 0.263 Chirality : 0.038 0.118 338 Planarity : 0.004 0.040 350 Dihedral : 3.774 17.893 309 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.37 % Allowed : 14.01 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.54), residues: 277 helix: 2.71 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.00 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.015 0.001 PHE R 289 TYR 0.017 0.002 TYR R 308 ARG 0.003 0.001 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.226 Fit side-chains REVERT: R 131 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7443 (ttt90) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.1122 time to fit residues: 5.6275 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 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 = 0.3699 r_free = 0.3699 target = 0.145678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131046 restraints weight = 3755.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133833 restraints weight = 1950.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135881 restraints weight = 1209.659| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2049 Z= 0.181 Angle : 0.508 5.157 2820 Z= 0.279 Chirality : 0.039 0.119 338 Planarity : 0.004 0.043 350 Dihedral : 3.826 17.689 309 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.10 % Allowed : 19.75 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.53), residues: 277 helix: 2.79 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 108 TYR 0.014 0.002 TYR R 141 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.206 Fit side-chains REVERT: R 131 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7453 (ttt90) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1135 time to fit residues: 4.9188 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 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 = 0.3661 r_free = 0.3661 target = 0.142324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127783 restraints weight = 3675.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130467 restraints weight = 1944.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132465 restraints weight = 1217.608| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2049 Z= 0.196 Angle : 0.513 4.890 2820 Z= 0.285 Chirality : 0.039 0.125 338 Planarity : 0.004 0.044 350 Dihedral : 3.939 18.079 309 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.01 % Allowed : 20.38 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.53), residues: 277 helix: 2.66 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -1.82 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.009 0.001 PHE R 289 TYR 0.013 0.002 TYR R 141 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.213 Fit side-chains REVERT: R 131 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7489 (ttt90) outliers start: 11 outliers final: 8 residues processed: 37 average time/residue: 0.1200 time to fit residues: 5.3745 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.144018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129435 restraints weight = 3757.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132188 restraints weight = 1948.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134070 restraints weight = 1208.524| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2049 Z= 0.155 Angle : 0.486 4.752 2820 Z= 0.268 Chirality : 0.038 0.123 338 Planarity : 0.003 0.040 350 Dihedral : 3.890 18.242 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.37 % Allowed : 21.66 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.53 (0.53), residues: 277 helix: 2.84 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -1.96 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.009 0.001 PHE R 289 TYR 0.013 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.234 Fit side-chains REVERT: R 131 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7442 (ttt90) outliers start: 10 outliers final: 10 residues processed: 32 average time/residue: 0.1165 time to fit residues: 4.6478 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 10 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.3904 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.146579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132321 restraints weight = 3698.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135156 restraints weight = 1915.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137157 restraints weight = 1176.295| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2049 Z= 0.136 Angle : 0.469 4.687 2820 Z= 0.256 Chirality : 0.038 0.119 338 Planarity : 0.003 0.034 350 Dihedral : 3.756 17.967 309 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 6.37 % Allowed : 21.66 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.55 (0.54), residues: 277 helix: 2.62 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.82 (0.84), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 289 TYR 0.011 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.202 Fit side-chains REVERT: R 131 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7449 (ttt90) outliers start: 10 outliers final: 10 residues processed: 35 average time/residue: 0.1136 time to fit residues: 4.9499 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.143354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128898 restraints weight = 3708.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131623 restraints weight = 1923.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133571 restraints weight = 1193.656| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2049 Z= 0.160 Angle : 0.498 6.284 2820 Z= 0.268 Chirality : 0.038 0.120 338 Planarity : 0.003 0.033 350 Dihedral : 3.827 17.893 309 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.37 % Allowed : 22.29 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.54), residues: 277 helix: 2.57 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.76 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.009 0.001 PHE R 289 TYR 0.012 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.209 Fit side-chains REVERT: R 131 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7459 (ttt90) outliers start: 10 outliers final: 10 residues processed: 34 average time/residue: 0.1343 time to fit residues: 5.4373 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.0980 chunk 24 optimal weight: 0.0670 chunk 14 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.147100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132780 restraints weight = 3739.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135578 restraints weight = 1944.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137646 restraints weight = 1192.262| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2049 Z= 0.130 Angle : 0.477 6.016 2820 Z= 0.254 Chirality : 0.038 0.120 338 Planarity : 0.003 0.031 350 Dihedral : 3.722 17.790 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.46 % Allowed : 24.20 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.54), residues: 277 helix: 2.62 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.82 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.007 0.001 PHE R 289 TYR 0.011 0.001 TYR R 174 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.230 Fit side-chains REVERT: R 131 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7418 (ttt90) outliers start: 7 outliers final: 7 residues processed: 36 average time/residue: 0.1068 time to fit residues: 4.7981 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129747 restraints weight = 3834.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132584 restraints weight = 1974.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134561 restraints weight = 1212.900| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2049 Z= 0.163 Angle : 0.494 5.689 2820 Z= 0.269 Chirality : 0.038 0.120 338 Planarity : 0.004 0.052 350 Dihedral : 3.813 17.673 309 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.73 % Allowed : 23.57 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.54), residues: 277 helix: 2.61 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.78 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.007 0.001 PHE R 290 TYR 0.012 0.001 TYR R 141 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.225 Fit side-chains REVERT: R 131 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7417 (ttt90) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.1143 time to fit residues: 4.9033 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.144948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130897 restraints weight = 3705.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133548 restraints weight = 1928.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135410 restraints weight = 1199.946| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.153 Angle : 0.490 5.596 2820 Z= 0.265 Chirality : 0.038 0.121 338 Planarity : 0.004 0.052 350 Dihedral : 3.797 17.816 309 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.10 % Allowed : 24.20 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.54), residues: 277 helix: 2.63 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.96 (0.84), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.006 0.001 PHE R 108 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.202 Fit side-chains REVERT: R 131 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7422 (ttt90) outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 0.1024 time to fit residues: 4.4394 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129104 restraints weight = 3773.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131803 restraints weight = 1961.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133753 restraints weight = 1217.787| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.155 Angle : 0.496 5.539 2820 Z= 0.269 Chirality : 0.038 0.121 338 Planarity : 0.004 0.051 350 Dihedral : 3.842 17.811 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.73 % Allowed : 25.48 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.54), residues: 277 helix: 2.64 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.02 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.009 0.003 HIS R 178 PHE 0.007 0.001 PHE R 289 TYR 0.012 0.001 TYR R 141 ARG 0.001 0.000 ARG R 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.47 seconds wall clock time: 19 minutes 16.20 seconds (1156.20 seconds total)