Starting phenix.real_space_refine on Mon Feb 10 19:56:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggp_40016/02_2025/8ggp_40016.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 13 5.16 5 C 1394 2.51 5 N 328 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2075 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2060 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 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: 2.37, per 1000 atoms: 1.14 Number of scatterers: 2075 At special positions: 0 Unit cell: (57.2682, 80.6961, 62.4744, 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 13 16.00 O 340 8.00 N 328 7.00 C 1394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 296.3 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.578A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.781A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.135A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 97 removed outlier: 4.202A pdb=" N PHE R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.501A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.778A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.520A pdb=" N ILE R 182 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.718A pdb=" N VAL R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.093A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.508A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.821A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 166 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 615 1.34 - 1.46: 495 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2131 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.569 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.537 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 2126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 2813 1.08 - 2.16: 100 2.16 - 3.25: 8 3.25 - 4.33: 7 4.33 - 5.41: 5 Bond angle restraints: 2933 Sorted by residual: angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.21 3.25 1.80e+00 3.09e-01 3.26e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.04 -5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" N VAL R 87 " pdb=" CA VAL R 87 " pdb=" C VAL R 87 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.86e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.13 -2.82 1.67e+00 3.59e-01 2.85e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.86 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.65: 1053 12.65 - 25.30: 111 25.30 - 37.95: 28 37.95 - 50.60: 12 50.60 - 63.25: 1 Dihedral angle restraints: 1205 sinusoidal: 378 harmonic: 827 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 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta harmonic sigma weight residual 180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.04e+00 dihedral pdb=" CA ARG R 151 " pdb=" CB ARG R 151 " pdb=" CG ARG R 151 " pdb=" CD ARG R 151 " ideal model delta sinusoidal sigma weight residual -180.00 -130.02 -49.98 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 1202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 226 0.030 - 0.059: 101 0.059 - 0.089: 25 0.089 - 0.119: 14 0.119 - 0.149: 1 Chirality restraints: 367 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 2.55 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA TRP R 313 " pdb=" N TRP R 313 " pdb=" C TRP R 313 " pdb=" CB TRP R 313 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 364 not shown) Planarity restraints: 351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.007 2.00e-02 2.50e+03 9.51e-03 2.26e+00 pdb=" CG TRP R 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO R 323 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO R 211 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.012 5.00e-02 4.00e+02 ... (remaining 348 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 590 2.82 - 3.34: 2039 3.34 - 3.86: 3309 3.86 - 4.38: 3397 4.38 - 4.90: 6312 Nonbonded interactions: 15647 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.298 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.305 3.120 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.344 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.491 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.513 3.120 ... (remaining 15642 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.550 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 0.051 2131 Z= 0.251 Angle : 0.520 5.412 2933 Z= 0.285 Chirality : 0.039 0.149 367 Planarity : 0.003 0.024 351 Dihedral : 12.492 63.247 664 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.51), residues: 276 helix: 1.93 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.52 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE R 217 TYR 0.010 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1090 time to fit residues: 2.6963 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116481 restraints weight = 2928.516| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.80 r_work: 0.3263 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2131 Z= 0.219 Angle : 0.487 5.460 2933 Z= 0.275 Chirality : 0.038 0.129 367 Planarity : 0.003 0.023 351 Dihedral : 4.328 17.921 309 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 5.15 % Favored : 93.81 % 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: 2.22 (0.51), residues: 276 helix: 2.12 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.69 (0.74), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.007 0.001 TYR R 174 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.234 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.1135 time to fit residues: 2.7146 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.130703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114174 restraints weight = 2882.733| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.82 r_work: 0.3248 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2131 Z= 0.227 Angle : 0.479 5.485 2933 Z= 0.270 Chirality : 0.038 0.128 367 Planarity : 0.003 0.024 351 Dihedral : 4.367 18.020 309 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.03 % Allowed : 10.31 % Favored : 88.66 % 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: 2.32 (0.51), residues: 276 helix: 2.22 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.79 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.008 0.001 TYR R 174 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.215 Fit side-chains REVERT: R 40 MET cc_start: 0.7294 (mtt) cc_final: 0.7031 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1794 time to fit residues: 3.6675 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116461 restraints weight = 2849.193| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.74 r_work: 0.3317 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2131 Z= 0.184 Angle : 0.450 5.446 2933 Z= 0.251 Chirality : 0.038 0.125 367 Planarity : 0.003 0.025 351 Dihedral : 4.230 18.075 309 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 13.92 % Favored : 85.05 % 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 (0.51), residues: 276 helix: 2.36 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.75 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.230 Fit side-chains REVERT: R 40 MET cc_start: 0.7194 (mtt) cc_final: 0.6952 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1983 time to fit residues: 4.0457 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111748 restraints weight = 2990.541| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.79 r_work: 0.3217 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2131 Z= 0.266 Angle : 0.494 5.519 2933 Z= 0.279 Chirality : 0.039 0.128 367 Planarity : 0.003 0.027 351 Dihedral : 4.413 17.814 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % 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: 2.29 (0.51), residues: 276 helix: 2.22 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.90 (0.74), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.221 Fit side-chains REVERT: R 40 MET cc_start: 0.7384 (mtt) cc_final: 0.7126 (mtt) REVERT: R 63 ARG cc_start: 0.5332 (ttm-80) cc_final: 0.4275 (ttm-80) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.1153 time to fit residues: 2.6828 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 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 = 0.3463 r_free = 0.3463 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115937 restraints weight = 2841.865| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.65 r_work: 0.3319 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2131 Z= 0.189 Angle : 0.450 5.480 2933 Z= 0.252 Chirality : 0.038 0.125 367 Planarity : 0.003 0.027 351 Dihedral : 4.252 18.341 309 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % 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 (0.51), residues: 276 helix: 2.40 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.86 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.006 0.001 TYR R 219 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.185 Fit side-chains REVERT: R 40 MET cc_start: 0.7216 (mtt) cc_final: 0.6952 (mtt) REVERT: R 63 ARG cc_start: 0.5006 (ttm-80) cc_final: 0.3887 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.1656 time to fit residues: 3.8546 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.132438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116790 restraints weight = 2913.728| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.70 r_work: 0.3328 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2131 Z= 0.170 Angle : 0.438 5.451 2933 Z= 0.245 Chirality : 0.037 0.123 367 Planarity : 0.003 0.027 351 Dihedral : 4.180 18.189 309 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 15.46 % Favored : 82.99 % 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: 2.67 (0.51), residues: 276 helix: 2.49 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.84 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.221 Fit side-chains REVERT: R 40 MET cc_start: 0.7132 (mtt) cc_final: 0.6896 (mtt) REVERT: R 63 ARG cc_start: 0.5045 (ttm-80) cc_final: 0.3885 (ttm-80) REVERT: R 115 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7788 (tp) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.1698 time to fit residues: 3.7316 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.132894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116843 restraints weight = 2958.580| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.79 r_work: 0.3322 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2131 Z= 0.175 Angle : 0.438 5.466 2933 Z= 0.245 Chirality : 0.037 0.122 367 Planarity : 0.003 0.027 351 Dihedral : 4.166 17.956 309 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % 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: 2.72 (0.51), residues: 276 helix: 2.54 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.88 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.204 Fit side-chains REVERT: R 40 MET cc_start: 0.7183 (mtt) cc_final: 0.6943 (mtt) REVERT: R 63 ARG cc_start: 0.5190 (ttm-80) cc_final: 0.3985 (ttm-80) REVERT: R 115 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7856 (tp) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.1684 time to fit residues: 3.8759 Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115279 restraints weight = 2978.709| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.75 r_work: 0.3263 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2131 Z= 0.212 Angle : 0.457 5.513 2933 Z= 0.257 Chirality : 0.038 0.123 367 Planarity : 0.003 0.027 351 Dihedral : 4.250 18.300 309 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.98 % Favored : 81.96 % 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: 2.59 (0.51), residues: 276 helix: 2.49 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -2.09 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.235 Fit side-chains REVERT: R 63 ARG cc_start: 0.5273 (ttm-80) cc_final: 0.4051 (ttm-80) REVERT: R 115 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7841 (tp) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.1037 time to fit residues: 2.5253 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 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 = 0.3440 r_free = 0.3440 target = 0.129431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113259 restraints weight = 2898.958| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.80 r_work: 0.3224 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2131 Z= 0.239 Angle : 0.471 5.533 2933 Z= 0.266 Chirality : 0.038 0.125 367 Planarity : 0.003 0.028 351 Dihedral : 4.328 18.202 309 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.98 % Favored : 81.96 % 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 (0.51), residues: 276 helix: 2.39 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -2.00 (0.73), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.216 Fit side-chains REVERT: R 63 ARG cc_start: 0.5374 (ttm-80) cc_final: 0.3679 (ttm170) REVERT: R 115 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7917 (tp) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.1125 time to fit residues: 2.7050 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.129471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113391 restraints weight = 2989.045| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.81 r_work: 0.3219 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2131 Z= 0.265 Angle : 0.489 5.566 2933 Z= 0.276 Chirality : 0.039 0.128 367 Planarity : 0.003 0.028 351 Dihedral : 4.422 18.333 309 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.58 % Allowed : 15.98 % Favored : 81.44 % 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: 2.34 (0.51), residues: 276 helix: 2.30 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -2.13 (0.70), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 132 ARG 0.001 0.000 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.07 seconds wall clock time: 26 minutes 22.80 seconds (1582.80 seconds total)