Starting phenix.real_space_refine on Tue Mar 3 11:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeu_13941/03_2026/7qeu_13941.map" } resolution = 2.7 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= 0.002 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 28 5.16 5 C 2011 2.51 5 N 468 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1419 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1514 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 0.91, per 1000 atoms: 0.30 Number of scatterers: 3002 At special positions: 0 Unit cell: (71.94, 67.58, 85.02, 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 28 16.00 O 495 8.00 N 468 7.00 C 2011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 82.1 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 77.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.561A pdb=" N ALA A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 101 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.557A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 removed outlier: 3.647A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 3.703A pdb=" N VAL B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.850A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.532A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 101 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.519A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 removed outlier: 3.518A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 215 hydrogen bonds defined for protein. 627 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: 0.48 Time building geometry restraints manager: 0.40 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: 865 1.34 - 1.46: 666 1.46 - 1.57: 1502 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3073 Sorted by residual: bond pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT B 402 " pdb=" C2 LMT B 402 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " ideal model delta sigma weight residual 1.529 1.565 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 4005 1.57 - 3.13: 97 3.13 - 4.70: 28 4.70 - 6.27: 19 6.27 - 7.83: 10 Bond angle restraints: 4159 Sorted by residual: angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.43 7.83 3.00e+00 1.11e-01 6.82e+00 angle pdb=" C6 LMT B 402 " pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " ideal model delta sigma weight residual 117.26 109.49 7.77 3.00e+00 1.11e-01 6.71e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" CA ARG B 75 " pdb=" CB ARG B 75 " pdb=" CG ARG B 75 " ideal model delta sigma weight residual 114.10 109.10 5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" C6 LMT B 401 " pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " ideal model delta sigma weight residual 117.26 109.76 7.50 3.00e+00 1.11e-01 6.25e+00 ... (remaining 4154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 1470 11.67 - 23.33: 199 23.33 - 35.00: 87 35.00 - 46.67: 18 46.67 - 58.33: 9 Dihedral angle restraints: 1783 sinusoidal: 720 harmonic: 1063 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " pdb=" CE MET B 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.06 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 220 0.028 - 0.055: 174 0.055 - 0.082: 48 0.082 - 0.110: 22 0.110 - 0.137: 7 Chirality restraints: 471 Sorted by residual: chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PRO B 173 " pdb=" N PRO B 173 " pdb=" C PRO B 173 " pdb=" CB PRO B 173 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 468 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " -0.014 2.00e-02 2.50e+03 7.43e-03 1.10e+00 pdb=" CG TYR B 65 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 174 " -0.015 5.00e-02 4.00e+02 2.32e-02 8.63e-01 pdb=" N PRO B 175 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.013 5.00e-02 4.00e+02 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 36 2.69 - 3.24: 2959 3.24 - 3.79: 4382 3.79 - 4.35: 5680 4.35 - 4.90: 9613 Nonbonded interactions: 22670 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.135 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.260 3.040 nonbonded pdb=" O CYS A 174 " pdb=" O HOH A 401 " model vdw 2.291 3.040 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 138 " model vdw 2.295 3.040 ... (remaining 22665 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 217 or (resid 301 and (name C4 or name C5 or na \ me C6 or name C7 or name C8 )) or resid 302 through 303)) selection = (chain 'B' and (resid 18 through 401 or (resid 402 and (name C3 or name C4 or na \ me C5 or name C6 or name C7 or name C8 )) or (resid 403 and (name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C18 or name C19 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C8 )))) } 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: 0.580 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.760 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.007 0.049 3079 Z= 0.321 Angle : 0.799 7.832 4171 Z= 0.376 Chirality : 0.043 0.137 471 Planarity : 0.003 0.029 494 Dihedral : 13.541 58.333 1075 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.43), residues: 351 helix: 0.99 (0.32), residues: 236 sheet: 1.25 (1.08), residues: 22 loop : -0.78 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.014 0.002 TYR B 65 PHE 0.013 0.001 PHE A 181 TRP 0.010 0.001 TRP A 24 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00742 ( 3073) covalent geometry : angle 0.79809 ( 4159) SS BOND : bond 0.00238 ( 6) SS BOND : angle 1.18189 ( 12) hydrogen bonds : bond 0.26966 ( 215) hydrogen bonds : angle 6.83498 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.111 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.7226 time to fit residues: 26.5863 Evaluate side-chains 30 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.081869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057492 restraints weight = 7910.864| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.37 r_work: 0.2807 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3079 Z= 0.156 Angle : 0.569 6.620 4171 Z= 0.317 Chirality : 0.043 0.140 471 Planarity : 0.004 0.030 494 Dihedral : 7.404 52.939 426 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 7.12 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.65 (0.45), residues: 351 helix: 2.64 (0.32), residues: 246 sheet: 1.42 (1.10), residues: 22 loop : -1.03 (0.71), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.010 0.002 TYR B 158 PHE 0.011 0.001 PHE B 31 TRP 0.007 0.001 TRP B 133 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3073) covalent geometry : angle 0.56745 ( 4159) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.05631 ( 12) hydrogen bonds : bond 0.07333 ( 215) hydrogen bonds : angle 4.09071 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7958 (tmt170) REVERT: B 42 GLU cc_start: 0.6763 (pp20) cc_final: 0.6442 (pp20) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.6085 time to fit residues: 25.5632 Evaluate side-chains 33 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.081071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056411 restraints weight = 8006.662| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.46 r_work: 0.2769 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3079 Z= 0.181 Angle : 0.571 6.282 4171 Z= 0.312 Chirality : 0.043 0.142 471 Planarity : 0.004 0.031 494 Dihedral : 6.743 42.819 426 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 11.46 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.91 (0.46), residues: 351 helix: 2.91 (0.32), residues: 245 sheet: 1.61 (1.14), residues: 22 loop : -1.18 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.011 0.002 TYR B 158 PHE 0.011 0.001 PHE B 31 TRP 0.007 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3073) covalent geometry : angle 0.56906 ( 4159) SS BOND : bond 0.00193 ( 6) SS BOND : angle 1.02695 ( 12) hydrogen bonds : bond 0.06575 ( 215) hydrogen bonds : angle 3.91913 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8220 (ttp80) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.6226 time to fit residues: 23.6641 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.083217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058802 restraints weight = 7979.680| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.45 r_work: 0.2837 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3079 Z= 0.123 Angle : 0.521 6.598 4171 Z= 0.282 Chirality : 0.041 0.145 471 Planarity : 0.003 0.031 494 Dihedral : 5.749 35.398 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 14.86 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.08 (0.46), residues: 351 helix: 2.97 (0.32), residues: 252 sheet: 1.85 (1.18), residues: 22 loop : -1.32 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.008 0.001 TYR A 155 PHE 0.010 0.001 PHE B 31 TRP 0.008 0.001 TRP A 133 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3073) covalent geometry : angle 0.51991 ( 4159) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.86874 ( 12) hydrogen bonds : bond 0.05083 ( 215) hydrogen bonds : angle 3.51529 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.114 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.6809 time to fit residues: 27.8675 Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.083080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058659 restraints weight = 7871.794| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.43 r_work: 0.2823 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3079 Z= 0.129 Angle : 0.525 6.197 4171 Z= 0.288 Chirality : 0.041 0.148 471 Planarity : 0.004 0.037 494 Dihedral : 5.417 32.374 426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 15.48 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.17 (0.47), residues: 351 helix: 3.02 (0.32), residues: 252 sheet: 1.98 (1.19), residues: 22 loop : -1.27 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 216 TYR 0.009 0.001 TYR A 158 PHE 0.011 0.001 PHE B 31 TRP 0.007 0.001 TRP B 133 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3073) covalent geometry : angle 0.52401 ( 4159) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.82142 ( 12) hydrogen bonds : bond 0.04981 ( 215) hydrogen bonds : angle 3.44630 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.150 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.5681 time to fit residues: 22.1720 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.083360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058927 restraints weight = 7924.098| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.43 r_work: 0.2827 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3079 Z= 0.124 Angle : 0.536 9.940 4171 Z= 0.284 Chirality : 0.040 0.142 471 Planarity : 0.004 0.037 494 Dihedral : 5.066 26.976 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 16.10 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.22 (0.46), residues: 351 helix: 3.07 (0.32), residues: 252 sheet: 1.99 (1.18), residues: 22 loop : -1.29 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 216 TYR 0.009 0.001 TYR A 158 PHE 0.010 0.001 PHE B 31 TRP 0.006 0.001 TRP B 133 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3073) covalent geometry : angle 0.53536 ( 4159) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.79935 ( 12) hydrogen bonds : bond 0.04794 ( 215) hydrogen bonds : angle 3.38254 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8111 (ttp80) REVERT: B 209 GLU cc_start: 0.9175 (tp30) cc_final: 0.8842 (tp30) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.6254 time to fit residues: 23.0982 Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 7 optimal weight: 0.0000 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 0.5124 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.085263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060898 restraints weight = 8006.425| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.46 r_work: 0.2881 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3079 Z= 0.106 Angle : 0.504 7.710 4171 Z= 0.267 Chirality : 0.039 0.138 471 Planarity : 0.003 0.031 494 Dihedral : 4.457 20.433 426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 16.72 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.36 (0.46), residues: 351 helix: 3.18 (0.31), residues: 252 sheet: 2.17 (1.21), residues: 22 loop : -1.29 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 216 TYR 0.008 0.001 TYR A 158 PHE 0.010 0.001 PHE B 31 TRP 0.007 0.001 TRP A 133 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3073) covalent geometry : angle 0.50318 ( 4159) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.77551 ( 12) hydrogen bonds : bond 0.04090 ( 215) hydrogen bonds : angle 3.21197 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.093 Fit side-chains REVERT: B 42 GLU cc_start: 0.6361 (pp20) cc_final: 0.5953 (pp20) REVERT: B 154 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: B 209 GLU cc_start: 0.9163 (tp30) cc_final: 0.8857 (tp30) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.5849 time to fit residues: 26.3769 Evaluate side-chains 35 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.084641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.060251 restraints weight = 8032.472| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.43 r_work: 0.2869 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3079 Z= 0.117 Angle : 0.545 8.196 4171 Z= 0.292 Chirality : 0.040 0.137 471 Planarity : 0.005 0.056 494 Dihedral : 4.403 18.819 426 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.93 % Allowed : 18.58 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.46), residues: 351 helix: 3.19 (0.31), residues: 252 sheet: 2.30 (1.22), residues: 22 loop : -1.29 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 216 TYR 0.015 0.001 TYR A 152 PHE 0.013 0.001 PHE B 31 TRP 0.006 0.001 TRP B 133 HIS 0.002 0.000 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3073) covalent geometry : angle 0.54422 ( 4159) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.75646 ( 12) hydrogen bonds : bond 0.04235 ( 215) hydrogen bonds : angle 3.25099 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.102 Fit side-chains REVERT: A 41 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8327 (tmmt) REVERT: B 154 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 209 GLU cc_start: 0.9176 (tp30) cc_final: 0.8847 (tp30) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.6598 time to fit residues: 22.9625 Evaluate side-chains 33 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.085126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060591 restraints weight = 8170.361| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.46 r_work: 0.2884 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3079 Z= 0.111 Angle : 0.526 7.888 4171 Z= 0.281 Chirality : 0.040 0.136 471 Planarity : 0.004 0.067 494 Dihedral : 4.222 17.546 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.93 % Allowed : 18.58 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.40 (0.46), residues: 351 helix: 3.19 (0.31), residues: 252 sheet: 2.39 (1.23), residues: 22 loop : -1.31 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.006 0.001 TYR A 158 PHE 0.010 0.001 PHE B 31 TRP 0.006 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3073) covalent geometry : angle 0.52518 ( 4159) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.73060 ( 12) hydrogen bonds : bond 0.04049 ( 215) hydrogen bonds : angle 3.21663 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.112 Fit side-chains REVERT: A 41 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8242 (tmmt) REVERT: B 209 GLU cc_start: 0.9161 (tp30) cc_final: 0.8891 (tp30) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.6961 time to fit residues: 24.9691 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.084828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060304 restraints weight = 7956.492| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.42 r_work: 0.2875 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3079 Z= 0.120 Angle : 0.565 8.994 4171 Z= 0.298 Chirality : 0.040 0.137 471 Planarity : 0.004 0.061 494 Dihedral : 4.207 18.098 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.46), residues: 351 helix: 3.19 (0.31), residues: 252 sheet: 2.36 (1.22), residues: 22 loop : -1.34 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 216 TYR 0.016 0.001 TYR A 152 PHE 0.011 0.001 PHE B 31 TRP 0.005 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3073) covalent geometry : angle 0.56409 ( 4159) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.73779 ( 12) hydrogen bonds : bond 0.04163 ( 215) hydrogen bonds : angle 3.23585 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.123 Fit side-chains REVERT: A 41 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8245 (tmmt) REVERT: B 209 GLU cc_start: 0.9155 (tp30) cc_final: 0.8849 (tp30) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.7140 time to fit residues: 26.3084 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.0470 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.085442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061130 restraints weight = 8011.027| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.42 r_work: 0.2894 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3079 Z= 0.116 Angle : 0.588 9.613 4171 Z= 0.300 Chirality : 0.039 0.137 471 Planarity : 0.005 0.070 494 Dihedral : 4.109 16.367 426 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.62 % Allowed : 19.50 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.40 (0.45), residues: 351 helix: 3.21 (0.31), residues: 252 sheet: 2.40 (1.22), residues: 22 loop : -1.40 (0.65), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 216 TYR 0.007 0.001 TYR A 158 PHE 0.010 0.001 PHE B 31 TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3073) covalent geometry : angle 0.58773 ( 4159) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.71431 ( 12) hydrogen bonds : bond 0.03955 ( 215) hydrogen bonds : angle 3.17069 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.77 seconds wall clock time: 23 minutes 21.12 seconds (1401.12 seconds total)