Starting phenix.real_space_refine on Thu Jul 2 04:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w26_65567/07_2026/9w26_65567.map" } resolution = 2.62 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= 0.023 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: 6 Type Number sf(0) Gaussians P 98 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 3679 2.51 5 N 1188 2.21 5 O 1419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1897 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 775 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 640 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.28 Number of scatterers: 6412 At special positions: 0 Unit cell: (74.736, 77.504, 99.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 98 15.00 Mg 1 11.99 O 1419 8.00 N 1188 7.00 C 3679 6.00 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: 0.65 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 69.4% alpha, 2.9% beta 33 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 66 through 97 Processing helix chain 'A' and resid 103 through 134 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.823A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.780A pdb=" N LYS A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.157A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.579A pdb=" N ARG A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.016A pdb=" N GLY A 306 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 65 through 97 Processing helix chain 'B' and resid 103 through 134 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.510A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.627A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 195 through 210 Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.851A pdb=" N GLY B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA3, first strand: chain 'B' and resid 234 through 235 277 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1673 1.34 - 1.45: 1660 1.45 - 1.57: 3168 1.57 - 1.69: 193 1.69 - 1.81: 49 Bond restraints: 6743 Sorted by residual: bond pdb=" C1' DT F 5 " pdb=" N1 DT F 5 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DT F 5 " pdb=" C2' DT F 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.01e+00 bond pdb=" C3' DT F 33 " pdb=" C2' DT F 33 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" C1' DC F 32 " pdb=" N1 DC F 32 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.27e+00 bond pdb=" C1' DT E 30 " pdb=" N1 DT E 30 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.03e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9288 2.14 - 4.28: 249 4.28 - 6.41: 8 6.41 - 8.55: 2 8.55 - 10.69: 1 Bond angle restraints: 9548 Sorted by residual: angle pdb=" CG1 VAL B 29 " pdb=" CB VAL B 29 " pdb=" CG2 VAL B 29 " ideal model delta sigma weight residual 110.80 121.49 -10.69 2.20e+00 2.07e-01 2.36e+01 angle pdb=" N3 DT D 4 " pdb=" C4 DT D 4 " pdb=" O4 DT D 4 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT F 28 " pdb=" C4 DT F 28 " pdb=" O4 DT F 28 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT E 28 " pdb=" C4 DT E 28 " pdb=" O4 DT E 28 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT D 17 " pdb=" C4 DT D 17 " pdb=" O4 DT D 17 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 9543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 3579 33.29 - 66.58: 325 66.58 - 99.87: 26 99.87 - 133.16: 0 133.16 - 166.45: 8 Dihedral angle restraints: 3938 sinusoidal: 2358 harmonic: 1580 Sorted by residual: dihedral pdb=" C4' DG F 30 " pdb=" C3' DG F 30 " pdb=" O3' DG F 30 " pdb=" P DC F 31 " ideal model delta sinusoidal sigma weight residual 220.00 53.55 166.45 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA F 8 " pdb=" C3' DA F 8 " pdb=" O3' DA F 8 " pdb=" P DA F 9 " ideal model delta sinusoidal sigma weight residual 220.00 54.92 165.08 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC F 12 " pdb=" C3' DC F 12 " pdb=" O3' DC F 12 " pdb=" P DG F 13 " ideal model delta sinusoidal sigma weight residual 220.00 55.42 164.58 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 3935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 1072 0.294 - 0.588: 2 0.588 - 0.882: 0 0.882 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL B 29 " pdb=" CA VAL B 29 " pdb=" CG1 VAL B 29 " pdb=" CG2 VAL B 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.16 -1.47 2.00e-01 2.50e+01 5.40e+01 chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" P G C 36 " pdb=" OP1 G C 36 " pdb=" OP2 G C 36 " pdb=" O5' G C 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 1072 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " 0.039 2.00e-02 2.50e+03 2.06e-02 9.53e+00 pdb=" N1 C C 8 " -0.046 2.00e-02 2.50e+03 pdb=" C2 C C 8 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 8 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 8 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C C 8 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C C 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 8 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 7 " -0.023 2.00e-02 2.50e+03 1.24e-02 3.47e+00 pdb=" N1 U C 7 " 0.028 2.00e-02 2.50e+03 pdb=" C2 U C 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U C 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U C 7 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U C 7 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U C 7 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 16 " 0.024 2.00e-02 2.50e+03 1.02e-02 3.09e+00 pdb=" N9 G C 16 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G C 16 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G C 16 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 16 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 16 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G C 16 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G C 16 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 16 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C 16 " -0.001 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 24 2.43 - 3.05: 4109 3.05 - 3.67: 10972 3.67 - 4.28: 16852 4.28 - 4.90: 25302 Nonbonded interactions: 57259 Sorted by model distance: nonbonded pdb=" OD1 ASP B 30 " pdb="MG MG B 401 " model vdw 1.816 2.170 nonbonded pdb=" OG SER A 170 " pdb=" OP2 C C 18 " model vdw 1.883 3.040 nonbonded pdb=" O3' DT D 22 " pdb="MG MG B 401 " model vdw 1.907 2.170 nonbonded pdb=" OP1 DC E 23 " pdb="MG MG B 401 " model vdw 1.935 2.170 nonbonded pdb=" NE2 HIS B 58 " pdb="MG MG B 401 " model vdw 2.066 2.250 ... (remaining 57254 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 0.045 6743 Z= 0.349 Angle : 0.685 10.688 9548 Z= 0.532 Chirality : 0.069 1.469 1075 Planarity : 0.004 0.066 873 Dihedral : 21.977 166.446 2918 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % 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: 3.20 (0.37), residues: 540 helix: 2.77 (0.27), residues: 335 sheet: -1.72 (0.87), residues: 30 loop : 1.73 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 286 TYR 0.019 0.001 TYR A 175 PHE 0.007 0.001 PHE B 269 TRP 0.004 0.001 TRP A 67 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.35 ( 6743) covalent geometry : angle 0.68525 / 0.53 ( 9548) hydrogen bonds : bond 0.11423 / 7.46 ( 359) hydrogen bonds : angle 4.41771 / 3.32 ( 952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.204 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.4724 time to fit residues: 24.7139 Evaluate side-chains 43 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.077015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060266 restraints weight = 18052.805| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.08 r_work: 0.3034 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6743 Z= 0.174 Angle : 0.613 7.091 9548 Z= 0.361 Chirality : 0.044 0.295 1075 Planarity : 0.004 0.022 873 Dihedral : 24.310 172.871 1824 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.75 % Allowed : 9.61 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.39 (0.36), residues: 540 helix: 2.89 (0.26), residues: 342 sheet: -1.33 (0.91), residues: 30 loop : 1.76 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.018 0.002 TYR B 175 PHE 0.011 0.001 PHE B 269 TRP 0.006 0.001 TRP B 309 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 6743) covalent geometry : angle 0.61275 / 0.36 ( 9548) hydrogen bonds : bond 0.05258 / 3.49 ( 359) hydrogen bonds : angle 3.69847 / 2.78 ( 952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.210 Fit side-chains REVERT: B 225 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8653 (tttt) REVERT: B 239 ASN cc_start: 0.8388 (p0) cc_final: 0.8043 (p0) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.5332 time to fit residues: 28.7165 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 0.0060 chunk 25 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060659 restraints weight = 18022.018| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.05 r_work: 0.3047 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6743 Z= 0.163 Angle : 0.579 7.271 9548 Z= 0.344 Chirality : 0.043 0.310 1075 Planarity : 0.003 0.024 873 Dihedral : 24.346 176.126 1824 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.18 % Allowed : 9.83 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.57 (0.36), residues: 540 helix: 3.01 (0.26), residues: 341 sheet: -1.40 (0.87), residues: 30 loop : 1.91 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.024 0.002 TYR A 175 PHE 0.009 0.001 PHE B 269 TRP 0.004 0.001 TRP B 309 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 6743) covalent geometry : angle 0.57930 / 0.34 ( 9548) hydrogen bonds : bond 0.04705 / 3.10 ( 359) hydrogen bonds : angle 3.50580 / 2.63 ( 952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.210 Fit side-chains REVERT: B 239 ASN cc_start: 0.8365 (p0) cc_final: 0.7920 (p0) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.4636 time to fit residues: 25.6975 Evaluate side-chains 44 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.079118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062621 restraints weight = 18175.799| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.11 r_work: 0.3106 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6743 Z= 0.137 Angle : 0.570 7.347 9548 Z= 0.335 Chirality : 0.042 0.323 1075 Planarity : 0.003 0.044 873 Dihedral : 24.367 178.889 1824 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.18 % Allowed : 11.14 % Favored : 86.68 % 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: 3.70 (0.36), residues: 540 helix: 3.07 (0.26), residues: 343 sheet: -1.59 (0.83), residues: 30 loop : 2.10 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.025 0.002 TYR A 175 PHE 0.006 0.001 PHE B 269 TRP 0.004 0.001 TRP B 203 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 ( 6743) covalent geometry : angle 0.56965 / 0.33 ( 9548) hydrogen bonds : bond 0.04335 / 2.88 ( 359) hydrogen bonds : angle 3.37849 / 2.52 ( 952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.210 Fit side-chains REVERT: A 157 LEU cc_start: 0.9232 (mp) cc_final: 0.9028 (mp) REVERT: B 239 ASN cc_start: 0.8362 (p0) cc_final: 0.7891 (p0) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.4423 time to fit residues: 24.5306 Evaluate side-chains 44 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.078043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061227 restraints weight = 18214.435| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3066 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6743 Z= 0.157 Angle : 0.578 7.699 9548 Z= 0.335 Chirality : 0.042 0.326 1075 Planarity : 0.003 0.039 873 Dihedral : 24.374 179.644 1824 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.75 % Allowed : 11.57 % Favored : 86.68 % 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: 3.68 (0.36), residues: 540 helix: 3.05 (0.26), residues: 343 sheet: -1.67 (0.82), residues: 30 loop : 2.13 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 286 TYR 0.022 0.002 TYR B 95 PHE 0.008 0.001 PHE B 269 TRP 0.004 0.001 TRP B 67 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 6743) covalent geometry : angle 0.57805 / 0.34 ( 9548) hydrogen bonds : bond 0.04385 / 2.91 ( 359) hydrogen bonds : angle 3.36621 / 2.51 ( 952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.208 Fit side-chains REVERT: B 239 ASN cc_start: 0.8292 (p0) cc_final: 0.8050 (p0) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.4757 time to fit residues: 24.3558 Evaluate side-chains 45 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060982 restraints weight = 18097.210| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.14 r_work: 0.3056 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6743 Z= 0.162 Angle : 0.576 7.926 9548 Z= 0.334 Chirality : 0.043 0.334 1075 Planarity : 0.004 0.050 873 Dihedral : 24.398 179.409 1824 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.97 % Allowed : 11.57 % Favored : 86.46 % 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: 3.62 (0.36), residues: 540 helix: 3.00 (0.26), residues: 343 sheet: -1.65 (0.84), residues: 30 loop : 2.10 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 286 TYR 0.023 0.002 TYR B 95 PHE 0.007 0.001 PHE B 36 TRP 0.003 0.001 TRP A 274 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 6743) covalent geometry : angle 0.57607 / 0.33 ( 9548) hydrogen bonds : bond 0.04323 / 2.85 ( 359) hydrogen bonds : angle 3.38040 / 2.53 ( 952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.274 Fit side-chains REVERT: A 157 LEU cc_start: 0.9267 (mp) cc_final: 0.9060 (mp) REVERT: B 225 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (tttt) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.4906 time to fit residues: 25.7607 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.078013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061221 restraints weight = 17997.553| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3065 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6743 Z= 0.155 Angle : 0.585 9.759 9548 Z= 0.335 Chirality : 0.043 0.341 1075 Planarity : 0.004 0.051 873 Dihedral : 24.421 178.426 1824 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.53 % Allowed : 12.66 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.60 (0.36), residues: 540 helix: 2.96 (0.26), residues: 343 sheet: -1.62 (0.83), residues: 30 loop : 2.14 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 286 TYR 0.025 0.002 TYR B 95 PHE 0.006 0.001 PHE B 36 TRP 0.003 0.001 TRP A 274 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 ( 6743) covalent geometry : angle 0.58478 / 0.33 ( 9548) hydrogen bonds : bond 0.04322 / 2.85 ( 359) hydrogen bonds : angle 3.37622 / 2.53 ( 952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.140 Fit side-chains REVERT: B 225 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8826 (tttt) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.4721 time to fit residues: 24.0353 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.078108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061315 restraints weight = 18042.975| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.14 r_work: 0.3069 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6743 Z= 0.154 Angle : 0.588 9.234 9548 Z= 0.335 Chirality : 0.043 0.346 1075 Planarity : 0.004 0.055 873 Dihedral : 24.438 177.612 1824 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.53 % Allowed : 13.10 % 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 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: 3.58 (0.36), residues: 540 helix: 2.94 (0.26), residues: 343 sheet: -1.53 (0.86), residues: 30 loop : 2.12 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.023 0.002 TYR B 95 PHE 0.006 0.001 PHE B 36 TRP 0.004 0.001 TRP A 67 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 6743) covalent geometry : angle 0.58835 / 0.34 ( 9548) hydrogen bonds : bond 0.04268 / 2.81 ( 359) hydrogen bonds : angle 3.37480 / 2.53 ( 952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.219 Fit side-chains REVERT: B 225 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8840 (tttt) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.4992 time to fit residues: 24.8998 Evaluate side-chains 45 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 0.0040 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.077027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060258 restraints weight = 18326.970| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.13 r_work: 0.3044 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6743 Z= 0.195 Angle : 0.626 11.584 9548 Z= 0.348 Chirality : 0.044 0.353 1075 Planarity : 0.004 0.062 873 Dihedral : 24.463 177.409 1824 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.09 % Allowed : 13.32 % Favored : 85.59 % 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: 3.44 (0.36), residues: 540 helix: 2.85 (0.26), residues: 343 sheet: -1.63 (0.87), residues: 30 loop : 2.02 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 286 TYR 0.023 0.002 TYR B 95 PHE 0.007 0.002 PHE B 36 TRP 0.004 0.001 TRP A 274 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 ( 6743) covalent geometry : angle 0.62580 / 0.35 ( 9548) hydrogen bonds : bond 0.04494 / 2.94 ( 359) hydrogen bonds : angle 3.48580 / 2.59 ( 952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.161 Fit side-chains REVERT: B 225 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8759 (tttt) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.4921 time to fit residues: 24.0469 Evaluate side-chains 45 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 37 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061595 restraints weight = 18108.170| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.17 r_work: 0.3086 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6743 Z= 0.137 Angle : 0.588 7.959 9548 Z= 0.335 Chirality : 0.042 0.352 1075 Planarity : 0.004 0.061 873 Dihedral : 24.478 176.103 1824 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.09 % Allowed : 13.54 % 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 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: 3.43 (0.36), residues: 540 helix: 2.84 (0.26), residues: 343 sheet: -1.74 (0.85), residues: 30 loop : 2.04 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.020 0.002 TYR B 95 PHE 0.006 0.001 PHE B 36 TRP 0.004 0.001 TRP A 67 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 ( 6743) covalent geometry : angle 0.58764 / 0.34 ( 9548) hydrogen bonds : bond 0.04256 / 2.81 ( 359) hydrogen bonds : angle 3.37779 / 2.53 ( 952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.190 Fit side-chains REVERT: B 225 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8753 (mtpt) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.5026 time to fit residues: 24.6001 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 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 = 0.3592 r_free = 0.3592 target = 0.078539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.061832 restraints weight = 18317.742| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.15 r_work: 0.3065 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 6743 Z= 0.232 Angle : 1.022 59.176 9548 Z= 0.622 Chirality : 0.044 0.392 1075 Planarity : 0.004 0.058 873 Dihedral : 24.477 176.119 1824 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.75 % Allowed : 12.66 % Favored : 85.59 % Cbeta Deviations : 0.20 % 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: 3.42 (0.36), residues: 540 helix: 2.84 (0.26), residues: 343 sheet: -1.74 (0.85), residues: 30 loop : 2.05 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.018 0.002 TYR B 95 PHE 0.009 0.001 PHE A 269 TRP 0.004 0.001 TRP A 67 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 ( 6743) covalent geometry : angle 1.02161 / 0.62 ( 9548) hydrogen bonds : bond 0.04258 / 2.81 ( 359) hydrogen bonds : angle 3.37440 / 2.53 ( 952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.15 seconds wall clock time: 37 minutes 57.54 seconds (2277.54 seconds total)