Starting phenix.real_space_refine on Fri Feb 14 19:31:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkq_12446/02_2025/7nkq_12446.cif" } resolution = 2.98 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= 0.001 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: 5 Type Number sf(0) Gaussians S 7 5.16 5 C 3278 2.51 5 N 946 2.21 5 O 1078 1.98 5 H 5312 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10621 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1500 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 917 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain breaks: 3 Chain: "C" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 643 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 3 Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 752 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 4 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 721 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain breaks: 2 Chain: "F" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 559 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 3 Chain: "d" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5002 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 10, 'TRANS': 319} Chain breaks: 1 Chain: "b" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 527 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 7.41, per 1000 atoms: 0.70 Number of scatterers: 10621 At special positions: 0 Unit cell: (112.05, 77.19, 83.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 1078 8.00 N 946 7.00 C 3278 6.00 H 5312 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 693.4 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 41.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 4.189A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.745A pdb=" N ILE B 15 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'd' and resid 110 through 137 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 222 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.876A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing helix chain 'b' and resid 131 through 160 removed outlier: 3.611A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 591 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: 3.71 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5310 1.03 - 1.23: 6 1.23 - 1.42: 2098 1.42 - 1.61: 3226 1.61 - 1.81: 12 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ARG E 63 " pdb=" CB ARG E 63 " ideal model delta sigma weight residual 1.528 1.502 0.027 2.61e-02 1.47e+03 1.05e+00 bond pdb=" CG GLU d 155 " pdb=" CD GLU d 155 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.23e-01 bond pdb=" CB ARG E 14 " pdb=" CG ARG E 14 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.20e-01 bond pdb=" CB ASP A 70 " pdb=" CG ASP A 70 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 bond pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.86e-01 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 17233 0.83 - 1.66: 1876 1.66 - 2.48: 134 2.48 - 3.31: 20 3.31 - 4.14: 19 Bond angle restraints: 19282 Sorted by residual: angle pdb=" N GLU d 155 " pdb=" CA GLU d 155 " pdb=" CB GLU d 155 " ideal model delta sigma weight residual 110.12 114.15 -4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" N GLU d 205 " pdb=" CA GLU d 205 " pdb=" CB GLU d 205 " ideal model delta sigma weight residual 110.12 113.26 -3.14 1.47e+00 4.63e-01 4.56e+00 angle pdb=" C LEU d 154 " pdb=" N GLU d 155 " pdb=" CA GLU d 155 " ideal model delta sigma weight residual 120.28 117.83 2.45 1.34e+00 5.57e-01 3.36e+00 angle pdb=" CA GLN d 112 " pdb=" CB GLN d 112 " pdb=" CG GLN d 112 " ideal model delta sigma weight residual 114.10 117.74 -3.64 2.00e+00 2.50e-01 3.32e+00 angle pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " ideal model delta sigma weight residual 112.60 115.61 -3.01 1.70e+00 3.46e-01 3.14e+00 ... (remaining 19277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4359 16.36 - 32.72: 406 32.72 - 49.08: 95 49.08 - 65.44: 44 65.44 - 81.80: 7 Dihedral angle restraints: 4911 sinusoidal: 2783 harmonic: 2128 Sorted by residual: dihedral pdb=" CA LEU d 409 " pdb=" C LEU d 409 " pdb=" N HIS d 410 " pdb=" CA HIS d 410 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP d 197 " pdb=" CB ASP d 197 " pdb=" CG ASP d 197 " pdb=" OD1 ASP d 197 " ideal model delta sinusoidal sigma weight residual -30.00 -88.29 58.29 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP b 163 " pdb=" CB ASP b 163 " pdb=" CG ASP b 163 " pdb=" OD1 ASP b 163 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 559 0.027 - 0.054: 197 0.054 - 0.082: 63 0.082 - 0.109: 45 0.109 - 0.136: 28 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA VAL B 74 " pdb=" N VAL B 74 " pdb=" C VAL B 74 " pdb=" CB VAL B 74 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA GLU C 16 " pdb=" N GLU C 16 " pdb=" C GLU C 16 " pdb=" CB GLU C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE d 428 " pdb=" N ILE d 428 " pdb=" C ILE d 428 " pdb=" CB ILE d 428 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 889 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP d 269 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP d 269 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP d 269 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA d 270 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN d 112 " -0.006 2.00e-02 2.50e+03 1.07e-02 1.70e+00 pdb=" CD GLN d 112 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN d 112 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN d 112 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN d 112 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN d 112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 275 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ALA d 275 " 0.022 2.00e-02 2.50e+03 pdb=" O ALA d 275 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG d 276 " -0.007 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 583 2.18 - 2.79: 22145 2.79 - 3.39: 30036 3.39 - 4.00: 38130 4.00 - 4.60: 58562 Nonbonded interactions: 149456 Sorted by model distance: nonbonded pdb=" O SER A 20 " pdb="HH12 ARG b 158 " model vdw 1.575 2.450 nonbonded pdb=" O ASN B 68 " pdb=" H GLY B 75 " model vdw 1.602 2.450 nonbonded pdb=" H ALA D 54 " pdb=" O ARG D 63 " model vdw 1.604 2.450 nonbonded pdb=" HH TYR d 401 " pdb=" OE1 GLU d 426 " model vdw 1.605 2.450 nonbonded pdb=" O GLU d 225 " pdb=" HZ1 LYS d 233 " model vdw 1.611 2.450 ... (remaining 149451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.070 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: 0.230 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.090 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 0.029 5340 Z= 0.274 Angle : 0.490 4.141 7215 Z= 0.264 Chirality : 0.041 0.136 892 Planarity : 0.003 0.033 945 Dihedral : 13.517 81.800 1951 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.34), residues: 662 helix: 1.88 (0.30), residues: 311 sheet: -0.90 (0.53), residues: 85 loop : 0.56 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.010 0.001 PHE d 150 TYR 0.011 0.002 TYR C 18 ARG 0.007 0.000 ARG d 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7632 (t0) cc_final: 0.7398 (t0) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 2.7323 time to fit residues: 211.0608 Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073777 restraints weight = 32097.399| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.98 r_work: 0.3082 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5340 Z= 0.223 Angle : 0.484 5.008 7215 Z= 0.255 Chirality : 0.040 0.135 892 Planarity : 0.004 0.046 945 Dihedral : 3.750 18.175 745 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.35 % Allowed : 8.54 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.34), residues: 662 helix: 2.26 (0.30), residues: 311 sheet: -1.32 (0.55), residues: 76 loop : 0.66 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.009 0.001 PHE d 187 TYR 0.010 0.002 TYR C 18 ARG 0.009 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8045 (t0) cc_final: 0.7634 (t0) REVERT: F 78 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7772 (mp0) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 1.9978 time to fit residues: 116.4241 Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073384 restraints weight = 32273.221| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.98 r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5340 Z= 0.256 Angle : 0.472 4.935 7215 Z= 0.247 Chirality : 0.040 0.131 892 Planarity : 0.004 0.061 945 Dihedral : 3.657 18.169 743 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.17 % Allowed : 9.93 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 662 helix: 2.35 (0.30), residues: 312 sheet: -1.48 (0.55), residues: 76 loop : 0.63 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS d 410 PHE 0.009 0.001 PHE d 187 TYR 0.009 0.002 TYR d 316 ARG 0.009 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8020 (t0) cc_final: 0.7598 (t0) REVERT: F 78 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7866 (mp0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 1.9880 time to fit residues: 107.7344 Evaluate side-chains 49 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 51 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.102243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074540 restraints weight = 32172.841| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.04 r_work: 0.3089 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5340 Z= 0.152 Angle : 0.442 4.909 7215 Z= 0.228 Chirality : 0.040 0.130 892 Planarity : 0.004 0.066 945 Dihedral : 3.445 17.054 743 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 9.93 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.35), residues: 662 helix: 2.55 (0.30), residues: 312 sheet: -1.59 (0.55), residues: 76 loop : 0.66 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS E 56 PHE 0.008 0.001 PHE d 150 TYR 0.008 0.002 TYR B 18 ARG 0.011 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7958 (t0) cc_final: 0.7486 (t0) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 1.9918 time to fit residues: 128.7273 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073354 restraints weight = 32070.532| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.00 r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5340 Z= 0.265 Angle : 0.473 5.105 7215 Z= 0.245 Chirality : 0.040 0.129 892 Planarity : 0.004 0.067 945 Dihedral : 3.481 17.154 743 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.70 % Allowed : 12.02 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.34), residues: 662 helix: 2.53 (0.29), residues: 312 sheet: -1.56 (0.55), residues: 76 loop : 0.55 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS E 56 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.009 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7910 (t0) cc_final: 0.7511 (t0) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 2.1182 time to fit residues: 118.9080 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073228 restraints weight = 32346.624| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.00 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5340 Z= 0.256 Angle : 0.470 5.161 7215 Z= 0.244 Chirality : 0.040 0.129 892 Planarity : 0.004 0.075 945 Dihedral : 3.507 17.298 743 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.87 % Allowed : 12.37 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.34), residues: 662 helix: 2.56 (0.29), residues: 312 sheet: -1.59 (0.56), residues: 76 loop : 0.53 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.009 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7922 (t0) cc_final: 0.7485 (t0) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 2.1587 time to fit residues: 118.9228 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073324 restraints weight = 32704.204| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.01 r_work: 0.3062 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5340 Z= 0.229 Angle : 0.464 5.108 7215 Z= 0.240 Chirality : 0.040 0.129 892 Planarity : 0.004 0.078 945 Dihedral : 3.482 17.187 743 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.87 % Allowed : 12.37 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.34), residues: 662 helix: 2.59 (0.29), residues: 312 sheet: -1.60 (0.56), residues: 76 loop : 0.54 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR B 18 ARG 0.010 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7959 (t0) cc_final: 0.7554 (t0) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 2.1232 time to fit residues: 121.0622 Evaluate side-chains 54 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072735 restraints weight = 32334.346| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.01 r_work: 0.3048 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5340 Z= 0.299 Angle : 0.487 5.230 7215 Z= 0.254 Chirality : 0.040 0.129 892 Planarity : 0.004 0.086 945 Dihedral : 3.585 17.611 743 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.05 % Allowed : 12.72 % Favored : 86.24 % 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: 1.74 (0.34), residues: 662 helix: 2.54 (0.29), residues: 312 sheet: -1.63 (0.56), residues: 76 loop : 0.48 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.004 0.001 HIS A 43 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7959 (t0) cc_final: 0.7508 (t0) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 2.1525 time to fit residues: 121.0812 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 22 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073305 restraints weight = 32507.159| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.04 r_work: 0.3059 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5340 Z= 0.207 Angle : 0.474 5.938 7215 Z= 0.245 Chirality : 0.040 0.130 892 Planarity : 0.004 0.087 945 Dihedral : 3.522 17.443 743 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.87 % Allowed : 13.76 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.35), residues: 662 helix: 2.62 (0.29), residues: 312 sheet: -1.68 (0.56), residues: 76 loop : 0.51 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR d 316 ARG 0.011 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7992 (t0) cc_final: 0.7563 (t0) outliers start: 5 outliers final: 6 residues processed: 51 average time/residue: 2.1449 time to fit residues: 115.6629 Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073115 restraints weight = 32342.612| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.01 r_work: 0.3063 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5340 Z= 0.252 Angle : 0.494 6.470 7215 Z= 0.255 Chirality : 0.040 0.128 892 Planarity : 0.004 0.089 945 Dihedral : 3.534 17.409 743 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 14.11 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.35), residues: 662 helix: 2.62 (0.29), residues: 312 sheet: -1.68 (0.56), residues: 76 loop : 0.52 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR B 18 ARG 0.011 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7999 (t0) cc_final: 0.7576 (t0) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 2.0978 time to fit residues: 111.3498 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 0.0770 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 overall best weight: 0.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN b 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074107 restraints weight = 32178.447| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.03 r_work: 0.3082 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5340 Z= 0.140 Angle : 0.472 6.320 7215 Z= 0.242 Chirality : 0.040 0.131 892 Planarity : 0.004 0.090 945 Dihedral : 3.417 16.935 743 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.52 % Allowed : 14.46 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.35), residues: 662 helix: 2.74 (0.30), residues: 312 sheet: -1.69 (0.56), residues: 76 loop : 0.58 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS E 56 PHE 0.007 0.001 PHE d 150 TYR 0.006 0.001 TYR B 18 ARG 0.011 0.000 ARG E 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8300.06 seconds wall clock time: 146 minutes 26.39 seconds (8786.39 seconds total)