Starting phenix.real_space_refine on Mon Feb 10 19:53:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggz_40026/02_2025/8ggz_40026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggz_40026/02_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_40026/02_2025/8ggz_40026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggz_40026/02_2025/8ggz_40026.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggz_40026/02_2025/8ggz_40026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggz_40026/02_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-5592/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: 2.69, per 1000 atoms: 1.35 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: 0.61 Conformation dependent library (CDL) restraints added in 277.7 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: 0.29 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: 0.53 Time building geometry restraints manager: 0.65 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- 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 : 0.206 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: 0.0991 time to fit residues: 5.9131 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 = 0.138532 restraints weight = 1858.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140607 restraints weight = 1140.620| |-----------------------------------------------------------------------------| 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 : 0.233 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: 0.1021 time to fit residues: 5.1198 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 : 0.227 ------------------------------------------------------------------------------- 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=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: 0.7980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130118 restraints weight = 3769.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132966 restraints weight = 1963.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134964 restraints weight = 1208.147| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2049 Z= 0.182 Angle : 0.514 5.171 2820 Z= 0.283 Chirality : 0.039 0.122 338 Planarity : 0.004 0.044 350 Dihedral : 3.881 17.704 309 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.73 % Allowed : 19.11 % 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 : -1.85 (0.72), residues: 70 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 0.010 0.001 PHE R 289 TYR 0.014 0.002 TYR R 141 ARG 0.002 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: 9 poor density : 30 time to evaluate : 0.207 Fit side-chains REVERT: R 131 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7454 (ttt90) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.1017 time to fit residues: 4.6071 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 : 0.221 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.142664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128151 restraints weight = 3666.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130792 restraints weight = 1946.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132787 restraints weight = 1223.021| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2049 Z= 0.181 Angle : 0.503 4.845 2820 Z= 0.279 Chirality : 0.039 0.125 338 Planarity : 0.004 0.042 350 Dihedral : 3.907 18.110 309 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.51 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: 2.49 (0.53), residues: 277 helix: 2.68 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -1.80 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.011 0.001 PHE R 289 TYR 0.012 0.001 TYR R 141 ARG 0.002 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 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.248 Fit side-chains REVERT: R 131 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7439 (ttt90) outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 0.1437 time to fit residues: 6.4019 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 : 0.355 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.145616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131045 restraints weight = 3737.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133770 restraints weight = 1947.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135855 restraints weight = 1211.517| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1949 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= 0.150 Angle : 0.484 4.701 2820 Z= 0.266 Chirality : 0.038 0.121 338 Planarity : 0.003 0.038 350 Dihedral : 3.873 18.257 309 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.10 % Allowed : 23.57 % 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: 2.56 (0.53), residues: 277 helix: 2.86 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -1.97 (0.71), residues: 73 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 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 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.247 Fit side-chains REVERT: R 131 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7447 (ttt90) outliers start: 8 outliers final: 8 residues processed: 32 average time/residue: 0.1145 time to fit residues: 4.5542 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.144059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129603 restraints weight = 3705.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132373 restraints weight = 1924.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134383 restraints weight = 1192.546| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2020 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 : 0.491 5.970 2820 Z= 0.265 Chirality : 0.038 0.119 338 Planarity : 0.003 0.033 350 Dihedral : 3.800 17.992 309 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 7.01 % Allowed : 21.02 % 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: 2.54 (0.54), residues: 277 helix: 2.73 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -1.83 (0.77), residues: 69 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 290 TYR 0.011 0.001 TYR R 308 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: 11 poor density : 28 time to evaluate : 0.242 Fit side-chains REVERT: R 131 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7425 (ttt90) outliers start: 11 outliers final: 10 residues processed: 35 average time/residue: 0.1070 time to fit residues: 4.6820 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 ILE 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 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: 0.1980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.143041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128430 restraints weight = 3707.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131263 restraints weight = 1943.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133162 restraints weight = 1202.187| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2110 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= 0.160 Angle : 0.492 5.238 2820 Z= 0.267 Chirality : 0.038 0.122 338 Planarity : 0.003 0.033 350 Dihedral : 3.867 17.969 309 Min Nonbonded Distance : 2.614 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: 2.52 (0.54), residues: 277 helix: 2.57 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.76 (0.86), 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 : 0.218 Fit side-chains REVERT: R 131 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7461 (ttt90) outliers start: 10 outliers final: 10 residues processed: 34 average time/residue: 0.1361 time to fit residues: 5.5320 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 : 0.227 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.142901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128440 restraints weight = 3790.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131157 restraints weight = 1955.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133127 restraints weight = 1211.144| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2191 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= 0.161 Angle : 0.492 5.032 2820 Z= 0.268 Chirality : 0.038 0.122 338 Planarity : 0.003 0.031 350 Dihedral : 3.876 18.003 309 Min Nonbonded Distance : 2.616 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: 2.46 (0.54), residues: 277 helix: 2.71 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -1.94 (0.77), 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 0.007 0.001 PHE R 289 TYR 0.011 0.001 TYR R 308 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: 10 poor density : 28 time to evaluate : 0.225 Fit side-chains REVERT: R 131 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7438 (ttt90) outliers start: 10 outliers final: 10 residues processed: 35 average time/residue: 0.1106 time to fit residues: 4.8049 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.147748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133275 restraints weight = 3802.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136084 restraints weight = 1972.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138181 restraints weight = 1212.773| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2125 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= 0.124 Angle : 0.472 4.715 2820 Z= 0.253 Chirality : 0.038 0.121 338 Planarity : 0.003 0.031 350 Dihedral : 3.743 17.888 309 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.46 % Allowed : 24.84 % 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: 2.53 (0.54), residues: 277 helix: 2.65 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.94 (0.85), residues: 64 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 0.012 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: 7 poor density : 30 time to evaluate : 0.227 Fit side-chains REVERT: R 131 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7422 (ttt90) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1095 time to fit residues: 4.6980 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain R residue 296 HIS 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: 0.2980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.144906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130686 restraints weight = 3695.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133373 restraints weight = 1925.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135281 restraints weight = 1202.090| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2226 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 : 0.485 4.706 2820 Z= 0.265 Chirality : 0.038 0.119 338 Planarity : 0.004 0.052 350 Dihedral : 3.828 17.650 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.10 % Allowed : 26.11 % 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: 2.56 (0.54), residues: 277 helix: 2.64 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.95 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.009 0.003 HIS R 178 PHE 0.006 0.001 PHE R 290 TYR 0.010 0.001 TYR R 174 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 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.211 Fit side-chains REVERT: R 131 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7422 (ttt90) outliers start: 8 outliers final: 8 residues processed: 33 average time/residue: 0.1098 time to fit residues: 4.4772 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 : 0.202 ------------------------------------------------------------------------------- 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 296 HIS 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: 0.3980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129396 restraints weight = 3782.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132125 restraints weight = 1981.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134080 restraints weight = 1226.993| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2278 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= 0.155 Angle : 0.494 4.740 2820 Z= 0.268 Chirality : 0.038 0.120 338 Planarity : 0.004 0.055 350 Dihedral : 3.865 17.712 309 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.10 % Allowed : 24.84 % Favored : 70.06 % 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 : -2.03 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.006 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: 1065.19 seconds wall clock time: 19 minutes 56.48 seconds (1196.48 seconds total)