Starting phenix.real_space_refine on Fri Apr 5 12:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggm_40013/04_2024/8ggm_40013_updated.pdb" } 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= 0.029 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 15 5.16 5 C 1473 2.51 5 N 352 2.21 5 O 371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2211 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2196 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 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: 1.86, per 1000 atoms: 0.84 Number of scatterers: 2211 At special positions: 0 Unit cell: (59.0036, 87.6377, 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 15 16.00 O 371 8.00 N 352 7.00 C 1473 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 - 3.50 Amino acid : False - 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: 0.93 Conformation dependent library (CDL) restraints added in 426.5 milliseconds 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.881A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.171A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.892A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.773A 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 179 through 185 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 237 Processing helix chain 'R' and resid 269 through 298 removed outlier: 4.219A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.589A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.607A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 154 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 664 1.35 - 1.46: 607 1.46 - 1.58: 978 1.58 - 1.70: 0 1.70 - 1.81: 21 Bond restraints: 2270 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.560 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.540 -0.034 2.00e-02 2.50e+03 2.89e+00 ... (remaining 2265 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.48: 67 107.48 - 114.12: 1332 114.12 - 120.76: 1061 120.76 - 127.40: 622 127.40 - 134.04: 27 Bond angle restraints: 3109 Sorted by residual: angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 125.51 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" C LEU R 84 " pdb=" N ALA R 85 " pdb=" CA ALA R 85 " ideal model delta sigma weight residual 122.42 119.35 3.07 1.55e+00 4.16e-01 3.93e+00 angle pdb=" C CYS R 285 " pdb=" N TRP R 286 " pdb=" CA TRP R 286 " ideal model delta sigma weight residual 122.11 119.06 3.05 1.64e+00 3.72e-01 3.45e+00 angle pdb=" CG ARG R 63 " pdb=" CD ARG R 63 " pdb=" NE ARG R 63 " ideal model delta sigma weight residual 112.00 116.00 -4.00 2.20e+00 2.07e-01 3.31e+00 angle pdb=" CA LEU R 144 " pdb=" CB LEU R 144 " pdb=" CG LEU R 144 " ideal model delta sigma weight residual 116.30 122.44 -6.14 3.50e+00 8.16e-02 3.07e+00 ... (remaining 3104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1177 16.67 - 33.33: 99 33.33 - 50.00: 17 50.00 - 66.67: 2 66.67 - 83.33: 3 Dihedral angle restraints: 1298 sinusoidal: 452 harmonic: 846 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 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASN R 51 " pdb=" CB ASN R 51 " pdb=" CG ASN R 51 " pdb=" OD1 ASN R 51 " ideal model delta sinusoidal sigma weight residual -90.00 -161.22 71.22 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 1295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 238 0.029 - 0.058: 87 0.058 - 0.087: 40 0.087 - 0.117: 12 0.117 - 0.146: 1 Chirality restraints: 378 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 2.54 -0.15 2.00e-01 2.50e+01 5.31e-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 2.40 0.11 2.00e-01 2.50e+01 3.12e-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 3.02e-01 ... (remaining 375 not shown) Planarity restraints: 374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO R 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 287 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO R 288 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO R 323 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.015 5.00e-02 4.00e+02 ... (remaining 371 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 615 2.82 - 3.34: 2187 3.34 - 3.86: 3536 3.86 - 4.38: 3742 4.38 - 4.90: 6879 Nonbonded interactions: 16959 Sorted by model distance: nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.297 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.384 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.444 2.440 nonbonded pdb=" O VAL R 295 " pdb=" N GLN R 299 " model vdw 2.501 2.520 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.547 2.520 ... (remaining 16954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 1.640 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: 7.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 0.052 2270 Z= 0.233 Angle : 0.540 6.137 3109 Z= 0.294 Chirality : 0.038 0.146 378 Planarity : 0.004 0.035 374 Dihedral : 13.214 83.331 745 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 2.21 (0.51), residues: 283 helix: 2.23 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.06 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.009 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2530 time to fit residues: 6.2841 Evaluate side-chains 20 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2270 Z= 0.235 Angle : 0.497 5.745 3109 Z= 0.275 Chirality : 0.040 0.130 378 Planarity : 0.004 0.029 374 Dihedral : 4.441 22.429 319 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.90 % Allowed : 8.52 % Favored : 90.58 % 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: 2.02 (0.50), residues: 283 helix: 1.97 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.13 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE R 290 TYR 0.008 0.001 TYR R 199 ARG 0.004 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.206 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.2158 time to fit residues: 6.2191 Evaluate side-chains 25 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2270 Z= 0.186 Angle : 0.455 5.183 3109 Z= 0.252 Chirality : 0.039 0.128 378 Planarity : 0.004 0.028 374 Dihedral : 4.304 21.913 319 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.35 % Allowed : 8.97 % Favored : 89.69 % 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: 2.38 (0.50), residues: 283 helix: 2.25 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -0.90 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 308 ARG 0.004 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.237 Fit side-chains REVERT: R 218 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8154 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.2019 time to fit residues: 6.1142 Evaluate side-chains 26 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2270 Z= 0.186 Angle : 0.453 5.261 3109 Z= 0.251 Chirality : 0.039 0.128 378 Planarity : 0.003 0.027 374 Dihedral : 4.270 21.872 319 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.90 % Allowed : 11.21 % Favored : 87.89 % 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: 2.36 (0.50), residues: 283 helix: 2.25 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -0.96 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.243 Fit side-chains REVERT: R 218 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8140 (m) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.2044 time to fit residues: 5.9559 Evaluate side-chains 26 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2270 Z= 0.167 Angle : 0.437 5.245 3109 Z= 0.241 Chirality : 0.038 0.125 378 Planarity : 0.003 0.027 374 Dihedral : 4.188 21.679 319 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 10.76 % Favored : 87.00 % 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: 2.45 (0.50), residues: 283 helix: 2.31 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -0.94 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.247 Fit side-chains REVERT: R 218 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (m) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.1937 time to fit residues: 6.5464 Evaluate side-chains 27 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 277 ILE 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 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2270 Z= 0.198 Angle : 0.474 8.188 3109 Z= 0.254 Chirality : 0.039 0.127 378 Planarity : 0.003 0.027 374 Dihedral : 4.255 21.880 319 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.55 % 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: 2.42 (0.49), residues: 283 helix: 2.29 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -0.96 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.220 Fit side-chains REVERT: R 218 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8125 (m) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1816 time to fit residues: 6.1307 Evaluate side-chains 27 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.0000 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2270 Z= 0.189 Angle : 0.469 8.038 3109 Z= 0.253 Chirality : 0.039 0.127 378 Planarity : 0.003 0.027 374 Dihedral : 4.234 21.880 319 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.14 % Allowed : 11.66 % Favored : 85.20 % 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: 2.39 (0.49), residues: 283 helix: 2.23 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -0.87 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.254 Fit side-chains REVERT: R 36 MET cc_start: 0.7299 (mtm) cc_final: 0.7044 (mtt) REVERT: R 218 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8142 (m) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.1779 time to fit residues: 5.8606 Evaluate side-chains 28 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2270 Z= 0.191 Angle : 0.470 7.848 3109 Z= 0.253 Chirality : 0.039 0.125 378 Planarity : 0.003 0.027 374 Dihedral : 4.236 21.891 319 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 12.11 % Favored : 85.65 % 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: 2.37 (0.49), residues: 283 helix: 2.22 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -0.88 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.186 Fit side-chains REVERT: R 36 MET cc_start: 0.7292 (mtm) cc_final: 0.7035 (mtt) REVERT: R 218 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8127 (m) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.1883 time to fit residues: 5.6476 Evaluate side-chains 28 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2270 Z= 0.172 Angle : 0.457 7.645 3109 Z= 0.246 Chirality : 0.038 0.123 378 Planarity : 0.003 0.026 374 Dihedral : 4.171 21.849 319 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 12.56 % Favored : 85.20 % 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: 2.48 (0.50), residues: 283 helix: 2.30 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -0.86 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.241 Fit side-chains REVERT: R 36 MET cc_start: 0.7273 (mtm) cc_final: 0.7048 (mtt) REVERT: R 218 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (m) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.1979 time to fit residues: 5.9893 Evaluate side-chains 27 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2270 Z= 0.235 Angle : 0.492 8.037 3109 Z= 0.268 Chirality : 0.040 0.129 378 Planarity : 0.003 0.027 374 Dihedral : 4.338 21.944 319 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.79 % Allowed : 13.45 % Favored : 84.75 % 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: 2.21 (0.49), residues: 283 helix: 2.12 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -0.98 (0.73), residues: 62 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 290 TYR 0.008 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.228 Fit side-chains REVERT: R 36 MET cc_start: 0.7364 (mtm) cc_final: 0.7108 (mtt) REVERT: R 218 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8101 (m) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1932 time to fit residues: 5.8388 Evaluate side-chains 27 residues out of total 254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092505 restraints weight = 2820.657| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.63 r_work: 0.2792 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2270 Z= 0.210 Angle : 0.477 7.760 3109 Z= 0.259 Chirality : 0.039 0.128 378 Planarity : 0.003 0.027 374 Dihedral : 4.275 22.005 319 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.79 % Allowed : 13.00 % Favored : 85.20 % 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: 2.25 (0.49), residues: 283 helix: 2.15 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -0.98 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 948.13 seconds wall clock time: 17 minutes 44.65 seconds (1064.65 seconds total)