Starting phenix.real_space_refine on Wed Sep 17 03:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9b_63960/09_2025/9u9b_63960.map" } resolution = 3.25 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= 0.010 sd= 0.051 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 32 5.16 5 C 2095 2.51 5 N 536 2.21 5 O 598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3261 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 97} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 96} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.02, per 1000 atoms: 0.31 Number of scatterers: 3261 At special positions: 0 Unit cell: (64.218, 70.056, 100.914, 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 32 16.00 O 598 8.00 N 536 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " 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: 0.19 Conformation dependent library (CDL) restraints added in 133.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 28.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 73 through 102 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'B' and resid 29 through 42 Processing helix chain 'B' and resid 72 through 101 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'H' and resid 26 through 31 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.177A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 150 removed outlier: 4.121A pdb=" N CYS A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 150 " --> pdb=" O CYS A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 126 removed outlier: 4.471A pdb=" N MET B 125 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.607A pdb=" N ALA H 92 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.607A pdb=" N ALA H 92 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL H 108 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.338A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.338A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 471 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: 0.32 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1008 1.35 - 1.47: 898 1.47 - 1.59: 1398 1.59 - 1.71: 0 1.71 - 1.83: 43 Bond restraints: 3347 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CB VAL L 95 " pdb=" CG2 VAL L 95 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.78e-01 bond pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.71e-01 bond pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.28e-01 bond pdb=" CB VAL L 18 " pdb=" CG2 VAL L 18 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.25e-01 ... (remaining 3342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 4307 1.04 - 2.08: 192 2.08 - 3.12: 49 3.12 - 4.17: 19 4.17 - 5.21: 4 Bond angle restraints: 4571 Sorted by residual: angle pdb=" CB LYS H 76 " pdb=" CG LYS H 76 " pdb=" CD LYS H 76 " ideal model delta sigma weight residual 111.30 116.51 -5.21 2.30e+00 1.89e-01 5.12e+00 angle pdb=" CA CYS A 147 " pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " ideal model delta sigma weight residual 114.40 118.91 -4.51 2.30e+00 1.89e-01 3.85e+00 angle pdb=" N CYS A 138 " pdb=" CA CYS A 138 " pdb=" C CYS A 138 " ideal model delta sigma weight residual 107.88 110.51 -2.63 1.41e+00 5.03e-01 3.48e+00 angle pdb=" CA PRO A 120 " pdb=" C PRO A 120 " pdb=" N CYS A 121 " ideal model delta sigma weight residual 114.75 117.45 -2.70 1.45e+00 4.76e-01 3.47e+00 angle pdb=" N ALA L 83 " pdb=" CA ALA L 83 " pdb=" C ALA L 83 " ideal model delta sigma weight residual 107.73 110.17 -2.44 1.34e+00 5.57e-01 3.30e+00 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1810 17.94 - 35.87: 120 35.87 - 53.81: 23 53.81 - 71.74: 8 71.74 - 89.68: 4 Dihedral angle restraints: 1965 sinusoidal: 716 harmonic: 1249 Sorted by residual: dihedral pdb=" CB CYS B 107 " pdb=" SG CYS B 107 " pdb=" SG CYS B 138 " pdb=" CB CYS B 138 " ideal model delta sinusoidal sigma weight residual -86.00 -9.38 -76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " pdb=" SG CYS A 137 " pdb=" CB CYS A 137 " ideal model delta sinusoidal sigma weight residual -86.00 -145.23 59.23 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 45.48 47.52 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 1962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 344 0.033 - 0.067: 130 0.067 - 0.100: 21 0.100 - 0.134: 21 0.134 - 0.167: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL B 106 " pdb=" N VAL B 106 " pdb=" C VAL B 106 " pdb=" CB VAL B 106 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 518 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 38 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO L 39 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 39 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 164 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" CD GLU B 164 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU B 164 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 122 " 0.140 9.50e-02 1.11e+02 6.27e-02 2.63e+00 pdb=" NE ARG B 122 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 122 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 122 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 122 " 0.002 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 209 2.73 - 3.27: 3317 3.27 - 3.81: 5429 3.81 - 4.36: 6271 4.36 - 4.90: 10879 Nonbonded interactions: 26105 Sorted by model distance: nonbonded pdb=" O GLY B 130 " pdb=" OG1 THR B 131 " model vdw 2.186 3.040 nonbonded pdb=" NH2 ARG L 60 " pdb=" OD1 ASP L 81 " model vdw 2.213 3.120 nonbonded pdb=" OG SER H 103 " pdb=" OD2 ASP H 107 " model vdw 2.222 3.040 nonbonded pdb=" O LEU A 39 " pdb=" NH1 ARG B 78 " model vdw 2.248 3.120 nonbonded pdb=" O LYS B 160 " pdb=" OE1 GLU B 164 " model vdw 2.288 3.040 ... (remaining 26100 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 28 through 29 or (resid 30 through 32 and (name N or name \ CA or name C or name O or name CB )) or resid 33 or (resid 34 through 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 37 or (res \ id 38 and (name N or name CA or name C or name O or name CB )) or resid 39 or (r \ esid 40 through 41 and (name N or name CA or name C or name O or name CB )) or r \ esid 42 through 74 or (resid 75 through 77 and (name N or name CA or name C or n \ ame O or name CB )) or resid 78 through 81 or (resid 82 through 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 through 87 or (resid 88 \ and (name N or name CA or name C or name O or name CB )) or resid 89 through 90 \ or (resid 91 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 2 or (resid 93 and (name N or name CA or name C or name O or name CB )) or resid \ 94 through 109 or (resid 110 and (name N or name CA or name C or name O or name \ CB )) or resid 116 through 143 or (resid 144 and (name N or name CA or name C o \ r name O or name CB )) or resid 145 through 168)) selection = (chain 'B' and (resid 28 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 42 or resid 72 through 73 or (resi \ d 74 through 77 and (name N or name CA or name C or name O or name CB )) or resi \ d 78 through 82 or (resid 83 through 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 126 or resid 133 through 168)) } 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: 2.600 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: 4.440 Find NCS groups from input model: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.032 3357 Z= 0.154 Angle : 0.590 5.207 4591 Z= 0.309 Chirality : 0.042 0.167 521 Planarity : 0.005 0.063 569 Dihedral : 13.351 89.681 1131 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.54 (0.42), residues: 423 helix: 2.71 (0.48), residues: 117 sheet: -0.27 (0.56), residues: 81 loop : -0.68 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.009 0.001 TYR H 33 PHE 0.010 0.001 PHE B 161 TRP 0.009 0.001 TRP A 36 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3347) covalent geometry : angle 0.57858 ( 4571) SS BOND : bond 0.00549 ( 10) SS BOND : angle 1.80840 ( 20) hydrogen bonds : bond 0.13279 ( 162) hydrogen bonds : angle 5.91374 ( 471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.101 Fit side-chains REVERT: A 155 SER cc_start: 0.6846 (p) cc_final: 0.6502 (t) REVERT: L 69 THR cc_start: 0.8505 (t) cc_final: 0.8007 (m) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0596 time to fit residues: 7.9635 Evaluate side-chains 91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.105798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089214 restraints weight = 6648.239| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.89 r_work: 0.3219 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3357 Z= 0.174 Angle : 0.640 6.912 4591 Z= 0.334 Chirality : 0.045 0.179 521 Planarity : 0.005 0.038 569 Dihedral : 4.688 19.185 459 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 1.75 % Allowed : 14.62 % Favored : 83.63 % 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 aren not related in a simple way. whole: 0.60 (0.43), residues: 423 helix: 2.80 (0.49), residues: 117 sheet: -0.39 (0.56), residues: 87 loop : -0.60 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 122 TYR 0.010 0.001 TYR H 33 PHE 0.018 0.002 PHE B 158 TRP 0.012 0.001 TRP B 156 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3347) covalent geometry : angle 0.63314 ( 4571) SS BOND : bond 0.00564 ( 10) SS BOND : angle 1.57426 ( 20) hydrogen bonds : bond 0.03629 ( 162) hydrogen bonds : angle 4.94909 ( 471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 155 SER cc_start: 0.7290 (p) cc_final: 0.6913 (t) REVERT: L 69 THR cc_start: 0.8764 (t) cc_final: 0.8313 (m) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.0636 time to fit residues: 7.7678 Evaluate side-chains 94 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.105816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089652 restraints weight = 6557.970| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.88 r_work: 0.3221 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3357 Z= 0.127 Angle : 0.591 7.811 4591 Z= 0.305 Chirality : 0.043 0.161 521 Planarity : 0.004 0.036 569 Dihedral : 4.578 18.807 459 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 2.63 % Allowed : 16.08 % Favored : 81.29 % 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 aren not related in a simple way. whole: 0.83 (0.43), residues: 423 helix: 3.26 (0.48), residues: 111 sheet: -0.52 (0.54), residues: 93 loop : -0.36 (0.45), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 122 TYR 0.010 0.001 TYR H 33 PHE 0.015 0.001 PHE B 158 TRP 0.010 0.001 TRP B 165 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3347) covalent geometry : angle 0.58652 ( 4571) SS BOND : bond 0.00403 ( 10) SS BOND : angle 1.28006 ( 20) hydrogen bonds : bond 0.03194 ( 162) hydrogen bonds : angle 4.65996 ( 471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 155 SER cc_start: 0.7263 (p) cc_final: 0.6978 (t) outliers start: 9 outliers final: 9 residues processed: 97 average time/residue: 0.0662 time to fit residues: 7.7582 Evaluate side-chains 98 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086237 restraints weight = 6563.724| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.87 r_work: 0.3159 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3357 Z= 0.170 Angle : 0.612 7.539 4591 Z= 0.319 Chirality : 0.044 0.214 521 Planarity : 0.004 0.032 569 Dihedral : 4.638 19.152 459 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.97 % Allowed : 16.67 % Favored : 78.36 % 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 aren not related in a simple way. whole: 0.59 (0.43), residues: 423 helix: 2.87 (0.49), residues: 117 sheet: -0.75 (0.49), residues: 108 loop : -0.41 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 60 TYR 0.010 0.001 TYR H 33 PHE 0.010 0.001 PHE B 158 TRP 0.014 0.001 TRP B 156 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3347) covalent geometry : angle 0.60639 ( 4571) SS BOND : bond 0.00463 ( 10) SS BOND : angle 1.35834 ( 20) hydrogen bonds : bond 0.03318 ( 162) hydrogen bonds : angle 4.58498 ( 471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 155 SER cc_start: 0.7442 (p) cc_final: 0.7143 (t) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.0616 time to fit residues: 7.7457 Evaluate side-chains 107 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.0070 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.0170 overall best weight: 0.1272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089668 restraints weight = 6495.279| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.89 r_work: 0.3225 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3357 Z= 0.105 Angle : 0.572 9.226 4591 Z= 0.293 Chirality : 0.041 0.137 521 Planarity : 0.004 0.034 569 Dihedral : 4.347 18.197 459 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 3.51 % Allowed : 21.35 % Favored : 75.15 % 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 aren not related in a simple way. whole: 0.72 (0.43), residues: 423 helix: 2.91 (0.48), residues: 117 sheet: -0.77 (0.48), residues: 114 loop : -0.18 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 122 TYR 0.010 0.001 TYR H 33 PHE 0.012 0.001 PHE B 158 TRP 0.012 0.001 TRP B 165 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 3347) covalent geometry : angle 0.56913 ( 4571) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.07358 ( 20) hydrogen bonds : bond 0.02927 ( 162) hydrogen bonds : angle 4.45331 ( 471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.133 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.0523 time to fit residues: 6.8089 Evaluate side-chains 100 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086795 restraints weight = 6569.065| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.85 r_work: 0.3174 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3357 Z= 0.160 Angle : 0.599 9.696 4591 Z= 0.309 Chirality : 0.043 0.190 521 Planarity : 0.004 0.031 569 Dihedral : 4.460 18.474 459 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.55 % Favored : 96.22 % Rotamer: Outliers : 4.68 % Allowed : 19.88 % Favored : 75.44 % 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 aren not related in a simple way. whole: 0.75 (0.44), residues: 423 helix: 2.95 (0.48), residues: 117 sheet: -0.74 (0.48), residues: 118 loop : -0.16 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 122 TYR 0.009 0.001 TYR L 48 PHE 0.009 0.001 PHE A 158 TRP 0.012 0.001 TRP B 156 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3347) covalent geometry : angle 0.59481 ( 4571) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.23593 ( 20) hydrogen bonds : bond 0.03203 ( 162) hydrogen bonds : angle 4.38025 ( 471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.175 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.0629 time to fit residues: 7.9731 Evaluate side-chains 103 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.104398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087611 restraints weight = 6601.259| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.91 r_work: 0.3187 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3357 Z= 0.124 Angle : 0.600 10.811 4591 Z= 0.306 Chirality : 0.042 0.148 521 Planarity : 0.004 0.032 569 Dihedral : 4.406 18.324 459 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 4.97 % Allowed : 19.59 % Favored : 75.44 % 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 aren not related in a simple way. whole: 0.79 (0.44), residues: 423 helix: 2.91 (0.48), residues: 117 sheet: -0.72 (0.48), residues: 118 loop : -0.08 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.009 0.001 TYR H 33 PHE 0.009 0.001 PHE B 158 TRP 0.010 0.001 TRP B 165 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3347) covalent geometry : angle 0.59243 ( 4571) SS BOND : bond 0.00371 ( 10) SS BOND : angle 1.55706 ( 20) hydrogen bonds : bond 0.03038 ( 162) hydrogen bonds : angle 4.35016 ( 471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.5986 (ttm) cc_final: 0.5586 (ttt) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.0645 time to fit residues: 8.1557 Evaluate side-chains 106 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.0000 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 overall best weight: 0.2562 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087789 restraints weight = 6858.202| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.95 r_work: 0.3186 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3357 Z= 0.114 Angle : 0.605 10.746 4591 Z= 0.306 Chirality : 0.041 0.130 521 Planarity : 0.004 0.031 569 Dihedral : 4.343 18.031 459 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.74 % Rotamer: Outliers : 4.09 % Allowed : 21.35 % Favored : 74.56 % 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 aren not related in a simple way. whole: 0.87 (0.44), residues: 423 helix: 2.96 (0.48), residues: 117 sheet: -0.63 (0.48), residues: 118 loop : -0.05 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.011 0.001 TYR H 33 PHE 0.012 0.001 PHE A 158 TRP 0.011 0.001 TRP B 165 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3347) covalent geometry : angle 0.59901 ( 4571) SS BOND : bond 0.00366 ( 10) SS BOND : angle 1.42749 ( 20) hydrogen bonds : bond 0.03031 ( 162) hydrogen bonds : angle 4.31016 ( 471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.6076 (ttm) cc_final: 0.5698 (ttt) REVERT: H 74 ASN cc_start: 0.7856 (m-40) cc_final: 0.7354 (m110) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.0731 time to fit residues: 9.0329 Evaluate side-chains 103 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.102624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086405 restraints weight = 6779.241| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.92 r_work: 0.3158 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3357 Z= 0.142 Angle : 0.629 10.655 4591 Z= 0.321 Chirality : 0.042 0.180 521 Planarity : 0.004 0.030 569 Dihedral : 4.447 17.891 459 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.55 % Favored : 96.22 % Rotamer: Outliers : 4.09 % Allowed : 21.64 % Favored : 74.27 % 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 aren not related in a simple way. whole: 0.76 (0.44), residues: 423 helix: 2.93 (0.48), residues: 117 sheet: -0.64 (0.47), residues: 124 loop : -0.18 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.010 0.001 TYR H 33 PHE 0.009 0.001 PHE H 80 TRP 0.018 0.001 TRP B 165 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3347) covalent geometry : angle 0.62227 ( 4571) SS BOND : bond 0.00406 ( 10) SS BOND : angle 1.48137 ( 20) hydrogen bonds : bond 0.03126 ( 162) hydrogen bonds : angle 4.31725 ( 471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.6079 (ttm) cc_final: 0.5692 (ttt) REVERT: B 165 TRP cc_start: 0.7002 (t60) cc_final: 0.6787 (t60) outliers start: 14 outliers final: 13 residues processed: 98 average time/residue: 0.0736 time to fit residues: 8.7358 Evaluate side-chains 102 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.104032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087992 restraints weight = 6734.469| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.93 r_work: 0.3190 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3357 Z= 0.115 Angle : 0.611 9.185 4591 Z= 0.309 Chirality : 0.041 0.131 521 Planarity : 0.004 0.032 569 Dihedral : 4.307 17.588 459 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.26 % Favored : 95.51 % Rotamer: Outliers : 3.80 % Allowed : 22.51 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.44), residues: 423 helix: 2.95 (0.48), residues: 117 sheet: -0.45 (0.50), residues: 114 loop : -0.33 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 122 TYR 0.010 0.001 TYR H 33 PHE 0.010 0.001 PHE A 158 TRP 0.016 0.001 TRP B 165 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3347) covalent geometry : angle 0.60622 ( 4571) SS BOND : bond 0.00332 ( 10) SS BOND : angle 1.34022 ( 20) hydrogen bonds : bond 0.02910 ( 162) hydrogen bonds : angle 4.22363 ( 471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.5974 (ttm) cc_final: 0.5597 (ttt) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.0691 time to fit residues: 8.1580 Evaluate side-chains 98 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.103170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086860 restraints weight = 6701.037| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.97 r_work: 0.3166 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3357 Z= 0.138 Angle : 0.623 10.173 4591 Z= 0.317 Chirality : 0.042 0.165 521 Planarity : 0.004 0.031 569 Dihedral : 4.388 17.534 459 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.55 % Favored : 96.22 % Rotamer: Outliers : 3.51 % Allowed : 22.22 % Favored : 74.27 % 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 aren not related in a simple way. whole: 0.81 (0.44), residues: 423 helix: 2.96 (0.48), residues: 117 sheet: -0.58 (0.47), residues: 124 loop : -0.17 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 122 TYR 0.009 0.001 TYR H 33 PHE 0.009 0.001 PHE H 80 TRP 0.012 0.001 TRP B 165 HIS 0.000 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3347) covalent geometry : angle 0.61779 ( 4571) SS BOND : bond 0.00385 ( 10) SS BOND : angle 1.40824 ( 20) hydrogen bonds : bond 0.03057 ( 162) hydrogen bonds : angle 4.26572 ( 471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.22 seconds wall clock time: 21 minutes 1.90 seconds (1261.90 seconds total)