Starting phenix.real_space_refine on Sat May 2 07:09:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.cif Found real_map, /net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.map" model { file = "/net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28vj_56885/05_2026/28vj_56885.cif" } resolution = 2.79 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= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2120 2.51 5 N 501 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3171 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2749 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.34 Number of scatterers: 3171 At special positions: 0 Unit cell: (70.125, 70.95, 70.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 534 8.00 N 501 7.00 C 2120 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: 0.28 Conformation dependent library (CDL) restraints added in 135.2 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 88.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.916A pdb=" N ALA A 59 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.716A pdb=" N VAL B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 65 removed outlier: 3.940A pdb=" N PHE B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Proline residue: B 56 - end of helix removed outlier: 3.593A pdb=" N LYS B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 88 Processing helix chain 'B' and resid 90 through 120 Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 151 removed outlier: 4.612A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 156 through 177 Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 224 through 234 Processing helix chain 'B' and resid 236 through 258 Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 267 through 289 Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.805A pdb=" N VAL B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 321 Proline residue: B 311 - end of helix Processing helix chain 'B' and resid 324 through 354 Proline residue: B 344 - end of helix removed outlier: 3.559A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 276 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 953 1.34 - 1.46: 817 1.46 - 1.58: 1444 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3245 Sorted by residual: bond pdb=" N ASP B 231 " pdb=" CA ASP B 231 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.38e+00 bond pdb=" N VAL B 25 " pdb=" CA VAL B 25 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.41e-02 5.03e+03 6.58e+00 bond pdb=" N ARG A 58 " pdb=" CA ARG A 58 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.06e+00 bond pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.19e-02 7.06e+03 4.72e+00 ... (remaining 3240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 4245 1.29 - 2.58: 114 2.58 - 3.87: 24 3.87 - 5.15: 10 5.15 - 6.44: 1 Bond angle restraints: 4394 Sorted by residual: angle pdb=" CA ALA A 59 " pdb=" C ALA A 59 " pdb=" N ARG A 60 " ideal model delta sigma weight residual 115.27 121.71 -6.44 1.30e+00 5.92e-01 2.46e+01 angle pdb=" CA ALA A 59 " pdb=" C ALA A 59 " pdb=" O ALA A 59 " ideal model delta sigma weight residual 121.81 116.83 4.98 1.18e+00 7.18e-01 1.78e+01 angle pdb=" N ARG A 58 " pdb=" CA ARG A 58 " pdb=" C ARG A 58 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" C ASN A 33 " pdb=" CA ASN A 33 " pdb=" CB ASN A 33 " ideal model delta sigma weight residual 117.23 112.60 4.63 1.36e+00 5.41e-01 1.16e+01 angle pdb=" CA SER B 92 " pdb=" C SER B 92 " pdb=" O SER B 92 " ideal model delta sigma weight residual 120.42 117.23 3.19 1.06e+00 8.90e-01 9.06e+00 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.21: 1566 14.21 - 28.42: 199 28.42 - 42.63: 73 42.63 - 56.84: 24 56.84 - 71.06: 3 Dihedral angle restraints: 1865 sinusoidal: 696 harmonic: 1169 Sorted by residual: dihedral pdb=" CD ARG A 60 " pdb=" NE ARG A 60 " pdb=" CZ ARG A 60 " pdb=" NH1 ARG A 60 " ideal model delta sinusoidal sigma weight residual 0.00 45.18 -45.18 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB MET B 95 " pdb=" CG MET B 95 " pdb=" SD MET B 95 " pdb=" CE MET B 95 " ideal model delta sinusoidal sigma weight residual -60.00 -118.80 58.80 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " pdb=" CG LYS B 3 " pdb=" CD LYS B 3 " ideal model delta sinusoidal sigma weight residual 60.00 118.45 -58.45 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 387 0.039 - 0.077: 99 0.077 - 0.116: 25 0.116 - 0.154: 6 0.154 - 0.193: 1 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA VAL B 25 " pdb=" N VAL B 25 " pdb=" C VAL B 25 " pdb=" CB VAL B 25 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 515 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 60 " 0.770 9.50e-02 1.11e+02 3.45e-01 7.26e+01 pdb=" NE ARG A 60 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 60 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 60 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 60 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 11 " -0.136 9.50e-02 1.11e+02 6.12e-02 2.64e+00 pdb=" NE ARG A 11 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 11 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 11 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 11 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 57 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ALA A 57 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA A 57 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 58 " 0.009 2.00e-02 2.50e+03 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1482 2.97 - 3.45: 3319 3.45 - 3.93: 5252 3.93 - 4.42: 6350 4.42 - 4.90: 10124 Nonbonded interactions: 26527 Sorted by model distance: nonbonded pdb=" OD1 ASP B 239 " pdb=" OH TYR B 292 " model vdw 2.486 3.040 nonbonded pdb=" O ILE B 116 " pdb=" OG SER B 120 " model vdw 2.499 3.040 nonbonded pdb=" OH TYR B 225 " pdb=" OG SER B 299 " model vdw 2.542 3.040 nonbonded pdb=" O MET B 263 " pdb=" O PHE B 266 " model vdw 2.584 3.040 nonbonded pdb=" O GLY B 348 " pdb=" OD1 ASP B 352 " model vdw 2.585 3.040 ... (remaining 26522 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.003 0.037 3245 Z= 0.185 Angle : 0.557 6.442 4394 Z= 0.334 Chirality : 0.039 0.193 518 Planarity : 0.016 0.345 537 Dihedral : 15.548 71.055 1119 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.60 % Allowed : 22.16 % Favored : 77.25 % 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: -0.78 (0.39), residues: 405 helix: -0.46 (0.26), residues: 339 sheet: 0.59 (1.68), residues: 14 loop : 0.11 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 11 TYR 0.005 0.001 TYR B 225 PHE 0.009 0.001 PHE B 140 TRP 0.003 0.001 TRP B 201 HIS 0.003 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3245) covalent geometry : angle 0.55709 ( 4394) hydrogen bonds : bond 0.21915 ( 276) hydrogen bonds : angle 8.55766 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.122 Fit side-chains REVERT: B 107 MET cc_start: 0.8864 (mtm) cc_final: 0.8636 (mtp) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.5626 time to fit residues: 29.5248 Evaluate side-chains 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111035 restraints weight = 3638.178| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.52 r_work: 0.3094 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3245 Z= 0.149 Angle : 0.547 6.120 4394 Z= 0.287 Chirality : 0.041 0.136 518 Planarity : 0.004 0.033 537 Dihedral : 4.029 16.077 437 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.59 % Allowed : 20.66 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.41), residues: 405 helix: 1.40 (0.27), residues: 342 sheet: 0.53 (1.28), residues: 21 loop : -0.38 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 11 TYR 0.008 0.001 TYR B 225 PHE 0.014 0.001 PHE B 16 TRP 0.002 0.001 TRP B 274 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3245) covalent geometry : angle 0.54685 ( 4394) hydrogen bonds : bond 0.04675 ( 276) hydrogen bonds : angle 4.86707 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.121 Fit side-chains REVERT: A 63 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6972 (mp0) REVERT: B 156 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6661 (mtt180) outliers start: 12 outliers final: 3 residues processed: 49 average time/residue: 0.6107 time to fit residues: 30.7673 Evaluate side-chains 48 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 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 = 0.3540 r_free = 0.3540 target = 0.137230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110482 restraints weight = 3632.516| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.53 r_work: 0.3086 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3245 Z= 0.152 Angle : 0.516 5.324 4394 Z= 0.268 Chirality : 0.041 0.132 518 Planarity : 0.004 0.034 537 Dihedral : 3.964 16.831 436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.89 % Allowed : 20.66 % Favored : 75.45 % 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: 2.36 (0.42), residues: 405 helix: 1.89 (0.28), residues: 342 sheet: 0.78 (1.23), residues: 21 loop : -0.58 (0.97), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.009 0.001 TYR B 225 PHE 0.016 0.001 PHE B 140 TRP 0.003 0.001 TRP B 293 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3245) covalent geometry : angle 0.51616 ( 4394) hydrogen bonds : bond 0.04382 ( 276) hydrogen bonds : angle 4.52739 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.121 Fit side-chains REVERT: A 65 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7868 (p90) REVERT: B 156 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6776 (mtt180) outliers start: 13 outliers final: 5 residues processed: 52 average time/residue: 0.5575 time to fit residues: 29.8509 Evaluate side-chains 49 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.138902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112635 restraints weight = 3640.441| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.45 r_work: 0.3111 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3245 Z= 0.145 Angle : 0.506 5.359 4394 Z= 0.262 Chirality : 0.041 0.136 518 Planarity : 0.004 0.034 537 Dihedral : 3.954 16.844 436 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.19 % Allowed : 21.86 % Favored : 73.95 % 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: 2.59 (0.43), residues: 405 helix: 2.07 (0.28), residues: 341 sheet: 0.89 (1.21), residues: 21 loop : -0.70 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.008 0.001 TYR B 225 PHE 0.017 0.001 PHE B 140 TRP 0.002 0.001 TRP B 293 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3245) covalent geometry : angle 0.50647 ( 4394) hydrogen bonds : bond 0.04109 ( 276) hydrogen bonds : angle 4.33395 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.101 Fit side-chains REVERT: A 65 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7807 (p90) REVERT: B 156 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6337 (mtt180) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 0.5148 time to fit residues: 28.6493 Evaluate side-chains 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112688 restraints weight = 3629.963| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.45 r_work: 0.3120 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3245 Z= 0.144 Angle : 0.503 5.365 4394 Z= 0.260 Chirality : 0.041 0.135 518 Planarity : 0.004 0.034 537 Dihedral : 3.939 17.025 436 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.29 % Allowed : 22.75 % Favored : 73.95 % 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: 2.67 (0.43), residues: 405 helix: 2.12 (0.28), residues: 342 sheet: 0.96 (1.20), residues: 21 loop : -0.70 (0.96), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.010 0.001 TYR B 225 PHE 0.017 0.001 PHE B 140 TRP 0.002 0.001 TRP B 201 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3245) covalent geometry : angle 0.50343 ( 4394) hydrogen bonds : bond 0.04043 ( 276) hydrogen bonds : angle 4.27933 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.075 Fit side-chains REVERT: A 65 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7826 (p90) REVERT: B 156 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6245 (mtt180) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.5849 time to fit residues: 30.0230 Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.138014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111753 restraints weight = 3630.092| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.45 r_work: 0.3117 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3245 Z= 0.146 Angle : 0.507 5.375 4394 Z= 0.262 Chirality : 0.041 0.134 518 Planarity : 0.004 0.034 537 Dihedral : 3.946 17.260 436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.19 % Allowed : 21.86 % Favored : 73.95 % 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: 2.70 (0.43), residues: 405 helix: 2.13 (0.28), residues: 342 sheet: 1.05 (1.21), residues: 21 loop : -0.73 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.010 0.001 TYR B 225 PHE 0.017 0.001 PHE B 140 TRP 0.003 0.001 TRP B 201 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3245) covalent geometry : angle 0.50703 ( 4394) hydrogen bonds : bond 0.04025 ( 276) hydrogen bonds : angle 4.25424 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.123 Fit side-chains REVERT: A 65 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7798 (p90) REVERT: B 156 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6233 (mtt180) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.5579 time to fit residues: 30.3710 Evaluate side-chains 54 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.138254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111868 restraints weight = 3697.057| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.47 r_work: 0.3118 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3245 Z= 0.143 Angle : 0.507 5.373 4394 Z= 0.261 Chirality : 0.041 0.135 518 Planarity : 0.004 0.034 537 Dihedral : 3.938 17.244 436 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.89 % Allowed : 22.16 % Favored : 73.95 % 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: 2.72 (0.43), residues: 405 helix: 2.16 (0.28), residues: 341 sheet: 1.03 (1.21), residues: 21 loop : -0.81 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.010 0.001 TYR B 225 PHE 0.016 0.001 PHE B 335 TRP 0.003 0.001 TRP B 293 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3245) covalent geometry : angle 0.50711 ( 4394) hydrogen bonds : bond 0.03983 ( 276) hydrogen bonds : angle 4.23527 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.119 Fit side-chains REVERT: A 65 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7792 (p90) REVERT: B 156 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6209 (mtt180) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.5785 time to fit residues: 30.9213 Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.137234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110932 restraints weight = 3751.338| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.48 r_work: 0.3094 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3245 Z= 0.161 Angle : 0.524 5.393 4394 Z= 0.270 Chirality : 0.042 0.139 518 Planarity : 0.004 0.034 537 Dihedral : 4.008 17.515 436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.59 % Allowed : 23.35 % Favored : 73.05 % 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: 2.63 (0.43), residues: 405 helix: 2.10 (0.28), residues: 341 sheet: 1.06 (1.21), residues: 21 loop : -0.79 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.010 0.001 TYR B 225 PHE 0.018 0.002 PHE B 335 TRP 0.005 0.001 TRP B 201 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3245) covalent geometry : angle 0.52394 ( 4394) hydrogen bonds : bond 0.04137 ( 276) hydrogen bonds : angle 4.28424 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.125 Fit side-chains REVERT: A 65 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7819 (p90) REVERT: B 156 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6256 (mtt180) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.5719 time to fit residues: 30.0125 Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113243 restraints weight = 3616.572| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.46 r_work: 0.3140 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3245 Z= 0.120 Angle : 0.493 5.348 4394 Z= 0.253 Chirality : 0.041 0.135 518 Planarity : 0.003 0.034 537 Dihedral : 3.876 17.117 436 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.59 % Allowed : 23.05 % Favored : 73.35 % 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: 2.87 (0.43), residues: 405 helix: 2.27 (0.29), residues: 341 sheet: 1.16 (1.21), residues: 21 loop : -0.85 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.009 0.001 TYR B 225 PHE 0.015 0.001 PHE B 140 TRP 0.005 0.001 TRP B 293 HIS 0.002 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3245) covalent geometry : angle 0.49283 ( 4394) hydrogen bonds : bond 0.03732 ( 276) hydrogen bonds : angle 4.16760 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.144 Fit side-chains REVERT: A 65 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7742 (p90) REVERT: B 156 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6227 (mtt180) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.6359 time to fit residues: 33.9544 Evaluate side-chains 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.138446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112272 restraints weight = 3625.481| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.45 r_work: 0.3125 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3245 Z= 0.140 Angle : 0.511 5.379 4394 Z= 0.263 Chirality : 0.041 0.139 518 Planarity : 0.004 0.034 537 Dihedral : 3.944 17.350 436 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.69 % Allowed : 24.25 % Favored : 73.05 % 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: 2.83 (0.43), residues: 405 helix: 2.23 (0.29), residues: 341 sheet: 1.31 (1.18), residues: 21 loop : -0.79 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.013 0.002 TYR B 235 PHE 0.017 0.001 PHE B 335 TRP 0.004 0.001 TRP B 201 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3245) covalent geometry : angle 0.51108 ( 4394) hydrogen bonds : bond 0.03903 ( 276) hydrogen bonds : angle 4.20289 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.124 Fit side-chains REVERT: A 65 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7849 (p90) REVERT: B 156 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6253 (mtt180) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.6778 time to fit residues: 34.7551 Evaluate side-chains 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 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 = 0.3559 r_free = 0.3559 target = 0.139047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112795 restraints weight = 3648.602| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.46 r_work: 0.3130 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3245 Z= 0.133 Angle : 0.508 5.378 4394 Z= 0.261 Chirality : 0.041 0.139 518 Planarity : 0.004 0.034 537 Dihedral : 3.932 17.248 436 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.99 % Allowed : 23.65 % Favored : 73.35 % 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: 2.89 (0.43), residues: 405 helix: 2.27 (0.29), residues: 341 sheet: 1.33 (1.18), residues: 21 loop : -0.79 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.016 0.002 TYR B 235 PHE 0.016 0.001 PHE B 140 TRP 0.004 0.001 TRP B 201 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3245) covalent geometry : angle 0.50819 ( 4394) hydrogen bonds : bond 0.03840 ( 276) hydrogen bonds : angle 4.18738 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.59 seconds wall clock time: 24 minutes 15.08 seconds (1455.08 seconds total)