Starting phenix.real_space_refine on Wed Mar 4 03:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_12446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_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 { model { file = "/net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_12446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_12446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_12446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkq_12446/03_2026/7nkq_12446.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.00, per 1000 atoms: 0.19 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: 0.80 Conformation dependent library (CDL) restraints added in 353.9 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: 0.20 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: 2.24 Time building geometry restraints manager: 1.17 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: 9.130 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- 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= 0.188 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG d 118 TYR 0.011 0.002 TYR C 18 PHE 0.010 0.001 PHE d 150 TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5340) covalent geometry : angle 0.48964 ( 7215) hydrogen bonds : bond 0.06304 ( 206) hydrogen bonds : angle 4.69352 ( 591) *********************** 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 : 0.317 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: 1.3502 time to fit residues: 103.6102 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 : 0.201 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.101122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073412 restraints weight = 32361.719| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.00 r_work: 0.3072 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5340 Z= 0.184 Angle : 0.493 4.936 7215 Z= 0.261 Chirality : 0.041 0.137 892 Planarity : 0.004 0.047 945 Dihedral : 3.798 18.385 745 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.34), residues: 662 helix: 2.21 (0.30), residues: 311 sheet: -1.30 (0.55), residues: 76 loop : 0.62 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 26 TYR 0.010 0.002 TYR C 18 PHE 0.009 0.001 PHE d 187 TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS d 410 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5340) covalent geometry : angle 0.49310 ( 7215) hydrogen bonds : bond 0.03727 ( 206) hydrogen bonds : angle 3.79708 ( 591) *********************** 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 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8054 (t0) cc_final: 0.7642 (t0) REVERT: F 78 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7769 (mp0) outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.9482 time to fit residues: 53.0292 Evaluate side-chains 48 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 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 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072842 restraints weight = 32597.740| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.04 r_work: 0.3054 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5340 Z= 0.205 Angle : 0.488 5.256 7215 Z= 0.256 Chirality : 0.041 0.131 892 Planarity : 0.004 0.069 945 Dihedral : 3.749 18.459 743 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.52 % Allowed : 9.23 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.34), residues: 662 helix: 2.29 (0.29), residues: 312 sheet: -1.49 (0.55), residues: 76 loop : 0.57 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 26 TYR 0.009 0.002 TYR d 316 PHE 0.009 0.001 PHE d 187 TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS d 410 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5340) covalent geometry : angle 0.48829 ( 7215) hydrogen bonds : bond 0.03506 ( 206) hydrogen bonds : angle 3.70566 ( 591) *********************** 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: 3 poor density : 48 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.8010 (t0) cc_final: 0.7591 (t0) REVERT: F 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7840 (mp0) outliers start: 3 outliers final: 0 residues processed: 50 average time/residue: 0.9624 time to fit residues: 50.7796 Evaluate side-chains 47 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073830 restraints weight = 32590.619| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.07 r_work: 0.3076 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5340 Z= 0.132 Angle : 0.453 5.081 7215 Z= 0.235 Chirality : 0.040 0.130 892 Planarity : 0.004 0.068 945 Dihedral : 3.542 17.440 743 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.05 % Allowed : 10.10 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.35), residues: 662 helix: 2.49 (0.29), residues: 312 sheet: -1.60 (0.55), residues: 76 loop : 0.64 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 26 TYR 0.007 0.002 TYR B 18 PHE 0.008 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5340) covalent geometry : angle 0.45350 ( 7215) hydrogen bonds : bond 0.03236 ( 206) hydrogen bonds : angle 3.46096 ( 591) *********************** 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 60 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7956 (t0) cc_final: 0.7526 (t0) REVERT: F 78 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (mm-30) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.9528 time to fit residues: 57.2932 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU 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 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.100855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073094 restraints weight = 32269.766| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.00 r_work: 0.3062 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5340 Z= 0.171 Angle : 0.473 5.358 7215 Z= 0.245 Chirality : 0.040 0.129 892 Planarity : 0.004 0.072 945 Dihedral : 3.555 17.523 743 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 11.85 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.34), residues: 662 helix: 2.51 (0.29), residues: 312 sheet: -1.62 (0.55), residues: 76 loop : 0.58 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 26 TYR 0.007 0.002 TYR B 18 PHE 0.009 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5340) covalent geometry : angle 0.47263 ( 7215) hydrogen bonds : bond 0.03248 ( 206) hydrogen bonds : angle 3.48818 ( 591) *********************** 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: 6 poor density : 49 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7954 (t0) cc_final: 0.7515 (t0) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 1.0489 time to fit residues: 55.1747 Evaluate side-chains 50 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR 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: 0.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.100559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072712 restraints weight = 32668.036| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.01 r_work: 0.3047 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5340 Z= 0.203 Angle : 0.491 6.612 7215 Z= 0.255 Chirality : 0.040 0.130 892 Planarity : 0.004 0.078 945 Dihedral : 3.625 17.586 743 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 12.37 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.34), residues: 662 helix: 2.47 (0.29), residues: 312 sheet: -1.62 (0.56), residues: 76 loop : 0.53 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 26 TYR 0.007 0.002 TYR B 18 PHE 0.009 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 5340) covalent geometry : angle 0.49117 ( 7215) hydrogen bonds : bond 0.03290 ( 206) hydrogen bonds : angle 3.52442 ( 591) *********************** 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 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7930 (t0) cc_final: 0.7487 (t0) REVERT: F 78 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7883 (mp0) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.9785 time to fit residues: 51.7186 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.101078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073401 restraints weight = 32147.027| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.01 r_work: 0.3063 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5340 Z= 0.140 Angle : 0.467 5.404 7215 Z= 0.242 Chirality : 0.040 0.129 892 Planarity : 0.004 0.081 945 Dihedral : 3.529 17.092 743 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.22 % Allowed : 13.59 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.35), residues: 662 helix: 2.60 (0.29), residues: 312 sheet: -1.67 (0.56), residues: 76 loop : 0.58 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 26 TYR 0.006 0.001 TYR B 18 PHE 0.008 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5340) covalent geometry : angle 0.46720 ( 7215) hydrogen bonds : bond 0.03166 ( 206) hydrogen bonds : angle 3.40069 ( 591) *********************** 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: 7 poor density : 50 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7928 (t0) cc_final: 0.7492 (t0) REVERT: F 78 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (mp0) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.0147 time to fit residues: 57.6645 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.100861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073116 restraints weight = 32255.708| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.01 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1333 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= 0.168 Angle : 0.475 5.165 7215 Z= 0.246 Chirality : 0.040 0.128 892 Planarity : 0.004 0.081 945 Dihedral : 3.536 17.122 743 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.05 % Allowed : 13.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.35), residues: 662 helix: 2.59 (0.29), residues: 312 sheet: -1.64 (0.57), residues: 76 loop : 0.56 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 26 TYR 0.006 0.001 TYR d 316 PHE 0.008 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5340) covalent geometry : angle 0.47515 ( 7215) hydrogen bonds : bond 0.03177 ( 206) hydrogen bonds : angle 3.42280 ( 591) *********************** 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 53 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7937 (t0) cc_final: 0.7498 (t0) REVERT: F 78 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7876 (mp0) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 1.0571 time to fit residues: 55.6019 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU 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 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.100894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073137 restraints weight = 32183.797| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.00 r_work: 0.3059 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5340 Z= 0.157 Angle : 0.469 5.203 7215 Z= 0.243 Chirality : 0.040 0.128 892 Planarity : 0.004 0.082 945 Dihedral : 3.504 17.045 743 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 14.46 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.35), residues: 662 helix: 2.62 (0.29), residues: 312 sheet: -1.62 (0.57), residues: 76 loop : 0.57 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 26 TYR 0.006 0.001 TYR B 18 PHE 0.008 0.001 PHE d 150 TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5340) covalent geometry : angle 0.46949 ( 7215) hydrogen bonds : bond 0.03139 ( 206) hydrogen bonds : angle 3.39442 ( 591) *********************** 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 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7930 (t0) cc_final: 0.7471 (t0) REVERT: F 78 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.9875 time to fit residues: 50.9449 Evaluate side-chains 52 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU 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 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 1 optimal weight: 0.1980 chunk 23 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 overall best weight: 0.1588 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.102214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074587 restraints weight = 31950.096| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.01 r_work: 0.3100 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5340 Z= 0.091 Angle : 0.457 6.712 7215 Z= 0.234 Chirality : 0.040 0.129 892 Planarity : 0.004 0.079 945 Dihedral : 3.321 16.193 743 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.87 % Allowed : 14.81 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.35), residues: 662 helix: 2.79 (0.30), residues: 312 sheet: -1.59 (0.57), residues: 76 loop : 0.65 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 26 TYR 0.004 0.001 TYR B 18 PHE 0.006 0.001 PHE d 150 TRP 0.002 0.000 TRP d 261 HIS 0.002 0.000 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 5340) covalent geometry : angle 0.45723 ( 7215) hydrogen bonds : bond 0.02941 ( 206) hydrogen bonds : angle 3.19701 ( 591) ********************** 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 58 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 78 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7902 (mp0) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 1.0394 time to fit residues: 61.1734 Evaluate side-chains 55 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain F residue 78 GLU 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 8 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 54 optimal weight: 0.0770 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 overall best weight: 0.2938 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.102054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074278 restraints weight = 32276.608| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.03 r_work: 0.3093 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5340 Z= 0.112 Angle : 0.487 11.098 7215 Z= 0.246 Chirality : 0.040 0.134 892 Planarity : 0.004 0.076 945 Dihedral : 3.308 16.124 743 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.70 % Allowed : 15.33 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.35), residues: 662 helix: 2.82 (0.29), residues: 312 sheet: -1.56 (0.58), residues: 76 loop : 0.63 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 26 TYR 0.004 0.001 TYR B 18 PHE 0.007 0.001 PHE d 150 TRP 0.002 0.000 TRP d 261 HIS 0.003 0.000 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5340) covalent geometry : angle 0.48666 ( 7215) hydrogen bonds : bond 0.02948 ( 206) hydrogen bonds : angle 3.19663 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.63 seconds wall clock time: 71 minutes 42.92 seconds (4302.92 seconds total)