Starting phenix.real_space_refine on Mon Feb 10 20:22:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_40013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_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/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_40013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_40013.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_40013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggm_40013/02_2025/8ggm_40013.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= 0.029 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. Time to flip 1 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: 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: 2.60, per 1000 atoms: 1.18 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 - 3.00 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: 0.63 Conformation dependent library (CDL) restraints added in 274.9 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... Secondary structure from input PDB file: 13 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.881A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 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 102 through 137 Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.614A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 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 removed outlier: 3.528A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 186 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 269 through 299 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 304 through 317 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) 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 340 173 hydrogen bonds defined for protein. 519 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: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 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: 0.00 - 1.23: 3004 1.23 - 2.45: 79 2.45 - 3.68: 15 3.68 - 4.91: 8 4.91 - 6.14: 3 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: 613 2.82 - 3.34: 2174 3.34 - 3.86: 3515 3.86 - 4.38: 3713 4.38 - 4.90: 6868 Nonbonded interactions: 16883 Sorted by model distance: nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.297 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.384 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.444 3.040 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.547 3.120 nonbonded pdb=" O ASN R 69 " pdb=" OG1 THR R 73 " model vdw 2.591 3.040 ... (remaining 16878 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.160 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- 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= 0.225 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 to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2805 time to fit residues: 6.9569 Evaluate side-chains 20 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.093996 restraints weight = 2829.169| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.57 r_work: 0.2821 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.212 Angle : 0.509 6.725 3109 Z= 0.283 Chirality : 0.040 0.128 378 Planarity : 0.004 0.029 374 Dihedral : 4.492 22.676 319 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.90 % Allowed : 7.17 % Favored : 91.93 % 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: 2.14 (0.50), residues: 283 helix: 2.02 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.03 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.004 0.000 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 23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.244 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.2167 time to fit residues: 5.5092 Evaluate side-chains 20 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092446 restraints weight = 2842.657| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.66 r_work: 0.2791 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- 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: 0.8528 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.212 Angle : 0.490 5.225 3109 Z= 0.273 Chirality : 0.040 0.129 378 Planarity : 0.004 0.028 374 Dihedral : 4.505 22.827 319 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.79 % Allowed : 8.97 % Favored : 89.24 % 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: 2.14 (0.50), residues: 283 helix: 2.02 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.07 (0.73), residues: 57 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 0.011 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.005 0.001 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 26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.222 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.2044 time to fit residues: 5.9184 Evaluate side-chains 24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.093486 restraints weight = 2829.487| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.54 r_work: 0.2813 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1218 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= 0.194 Angle : 0.496 8.534 3109 Z= 0.268 Chirality : 0.039 0.128 378 Planarity : 0.003 0.027 374 Dihedral : 4.407 22.797 319 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.90 % Allowed : 11.66 % Favored : 87.44 % 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: 2.42 (0.50), residues: 283 helix: 2.12 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.74 (0.81), residues: 53 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 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 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 24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.250 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.2179 time to fit residues: 5.7888 Evaluate side-chains 23 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 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 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092115 restraints weight = 2846.111| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.64 r_work: 0.2788 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 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 = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.206 Angle : 0.495 8.260 3109 Z= 0.270 Chirality : 0.040 0.128 378 Planarity : 0.004 0.028 374 Dihedral : 4.410 22.885 319 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.35 % Allowed : 12.56 % Favored : 86.10 % 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: 2.44 (0.50), residues: 283 helix: 2.13 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.69 (0.81), residues: 53 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 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 131 *********************** 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 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.229 Fit side-chains REVERT: R 36 MET cc_start: 0.7142 (mtm) cc_final: 0.6926 (mtt) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.2096 time to fit residues: 5.8227 Evaluate side-chains 24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.095520 restraints weight = 2810.054| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.54 r_work: 0.2845 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1308 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= 0.165 Angle : 0.469 7.656 3109 Z= 0.254 Chirality : 0.038 0.125 378 Planarity : 0.003 0.027 374 Dihedral : 4.258 22.658 319 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 2.61 (0.50), residues: 283 helix: 2.25 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.65 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 290 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** 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 27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.227 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2002 time to fit residues: 6.0939 Evaluate side-chains 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 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 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.092935 restraints weight = 2875.631| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.56 r_work: 0.2806 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.207 Angle : 0.486 7.793 3109 Z= 0.266 Chirality : 0.039 0.126 378 Planarity : 0.003 0.027 374 Dihedral : 4.361 22.701 319 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 11.66 % Favored : 86.10 % 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 (0.50), residues: 283 helix: 2.18 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.66 (0.81), residues: 53 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 0.010 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 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 27 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.247 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2039 time to fit residues: 6.2001 Evaluate side-chains 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.092580 restraints weight = 2931.618| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.57 r_work: 0.2811 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.203 Angle : 0.489 7.649 3109 Z= 0.268 Chirality : 0.039 0.126 378 Planarity : 0.003 0.027 374 Dihedral : 4.364 22.827 319 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 2.52 (0.50), residues: 283 helix: 2.20 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.75 (0.78), residues: 53 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 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** 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 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.218 Fit side-chains REVERT: R 36 MET cc_start: 0.7046 (mtt) cc_final: 0.6832 (mtt) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.2106 time to fit residues: 5.9116 Evaluate side-chains 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 16 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.095911 restraints weight = 2796.976| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.64 r_work: 0.2848 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2270 Z= 0.154 Angle : 0.459 7.175 3109 Z= 0.250 Chirality : 0.038 0.123 378 Planarity : 0.003 0.026 374 Dihedral : 4.215 22.703 319 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.35 % Allowed : 13.45 % 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: 2.69 (0.50), residues: 283 helix: 2.33 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.79 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 290 TYR 0.006 0.001 TYR R 209 ARG 0.000 0.000 ARG R 151 *********************** 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 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.219 Fit side-chains REVERT: R 36 MET cc_start: 0.7154 (mtt) cc_final: 0.6901 (mtt) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.2131 time to fit residues: 5.9073 Evaluate side-chains 24 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.092395 restraints weight = 2851.705| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.55 r_work: 0.2797 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2270 Z= 0.217 Angle : 0.494 7.682 3109 Z= 0.271 Chirality : 0.040 0.127 378 Planarity : 0.003 0.027 374 Dihedral : 4.378 22.692 319 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.30 % 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 (0.50), residues: 283 helix: 2.19 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.80 (0.77), residues: 53 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 0.007 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 28 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.249 Fit side-chains REVERT: R 36 MET cc_start: 0.7070 (mtt) cc_final: 0.6811 (mtt) REVERT: R 228 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.8303 (ttt-90) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2038 time to fit residues: 6.1930 Evaluate side-chains 26 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 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 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.092043 restraints weight = 2818.401| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.64 r_work: 0.2787 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 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 = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1492 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= 0.214 Angle : 0.492 7.481 3109 Z= 0.270 Chirality : 0.039 0.127 378 Planarity : 0.003 0.027 374 Dihedral : 4.393 22.941 319 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.79 % Allowed : 13.90 % Favored : 84.30 % 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: 2.18 (0.34), residues: 230 sheet: None (None), residues: 0 loop : -0.79 (0.77), residues: 53 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 290 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.95 seconds wall clock time: 29 minutes 51.56 seconds (1791.56 seconds total)