Starting phenix.real_space_refine on Tue Feb 3 13:13:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.map" model { file = "/net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oa6_70274/02_2026/9oa6_70274.cif" } resolution = 3.9 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 25 5.16 5 C 1869 2.51 5 N 498 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2909 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 234} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1675 SG CYS A 106 64.977 29.801 46.108 1.00122.40 S ATOM 1693 SG CYS A 109 63.179 26.533 45.413 1.00131.24 S ATOM 1832 SG CYS A 126 61.065 29.783 45.875 1.00127.99 S ATOM 1791 SG CYS A 120 56.870 25.975 53.311 1.00123.40 S ATOM 1810 SG CYS A 123 56.447 22.438 51.890 1.00137.49 S ATOM 1952 SG CYS A 140 54.154 25.379 50.846 1.00129.37 S Time building chain proxies: 0.67, per 1000 atoms: 0.23 Number of scatterers: 2909 At special positions: 0 Unit cell: (90.688, 60.736, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 25 16.00 O 515 8.00 N 498 7.00 C 1869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 64.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 119 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 106 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 109 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 126 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 133 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 140 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 123 " Number of angles added : 6 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 688 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 50.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.556A pdb=" N LEU B 34 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'B' and resid 39 through 59 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.201A pdb=" N LEU B 80 " --> pdb=" O TYR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 104 Processing helix chain 'A' and resid 21 through 35 removed outlier: 4.069A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 145 through 167 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 182 through 213 removed outlier: 3.811A pdb=" N THR A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 236 through 245 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 14 removed outlier: 4.121A pdb=" N VAL B 12 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 123 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.612A pdb=" N VAL A 94 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.864A pdb=" N HIS A 132 " --> pdb=" O ILE A 141 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 360 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: 0.22 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 942 1.34 - 1.46: 687 1.46 - 1.58: 1314 1.58 - 1.70: 0 1.70 - 1.81: 33 Bond restraints: 2976 Sorted by residual: bond pdb=" CB GLU B 58 " pdb=" CG GLU B 58 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB GLU A 95 " pdb=" CG GLU A 95 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB LYS B 29 " pdb=" CG LYS B 29 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.67e-01 bond pdb=" CA GLU B 58 " pdb=" CB GLU B 58 " ideal model delta sigma weight residual 1.534 1.547 -0.013 1.58e-02 4.01e+03 6.95e-01 bond pdb=" CA THR B 74 " pdb=" C THR B 74 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.56e-02 4.11e+03 6.57e-01 ... (remaining 2971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 3749 1.47 - 2.93: 207 2.93 - 4.40: 52 4.40 - 5.87: 18 5.87 - 7.33: 6 Bond angle restraints: 4032 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 111.90 108.52 3.38 8.10e-01 1.52e+00 1.74e+01 angle pdb=" N SER A 118 " pdb=" CA SER A 118 " pdb=" C SER A 118 " ideal model delta sigma weight residual 108.24 112.43 -4.19 1.32e+00 5.74e-01 1.01e+01 angle pdb=" CA GLU B 58 " pdb=" CB GLU B 58 " pdb=" CG GLU B 58 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA ARG A 215 " pdb=" CB ARG A 215 " pdb=" CG ARG A 215 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.28e+00 angle pdb=" C LYS B 103 " pdb=" N ILE B 104 " pdb=" CA ILE B 104 " ideal model delta sigma weight residual 123.16 120.16 3.00 1.06e+00 8.90e-01 7.98e+00 ... (remaining 4027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 1602 17.09 - 34.17: 133 34.17 - 51.26: 27 51.26 - 68.34: 3 68.34 - 85.43: 4 Dihedral angle restraints: 1769 sinusoidal: 699 harmonic: 1070 Sorted by residual: dihedral pdb=" CA GLY A 214 " pdb=" C GLY A 214 " pdb=" N ARG A 215 " pdb=" CA ARG A 215 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA CYS A 126 " pdb=" C CYS A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 1766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 313 0.046 - 0.091: 106 0.091 - 0.137: 26 0.137 - 0.183: 2 0.183 - 0.228: 1 Chirality restraints: 448 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 39 " pdb=" CB LEU A 39 " pdb=" CD1 LEU A 39 " pdb=" CD2 LEU A 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA THR A 217 " pdb=" N THR A 217 " pdb=" C THR A 217 " pdb=" CB THR A 217 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 445 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 249 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO A 250 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 36 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 37 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 163 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C VAL A 163 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 163 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 164 " 0.011 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1518 2.98 - 3.46: 3226 3.46 - 3.94: 4435 3.94 - 4.42: 5040 4.42 - 4.90: 7850 Nonbonded interactions: 22069 Sorted by model distance: nonbonded pdb=" ND1 HIS A 119 " pdb="ZN ZN A 801 " model vdw 2.499 1.848 nonbonded pdb=" N GLU A 95 " pdb=" OE1 GLU A 95 " model vdw 2.558 3.120 nonbonded pdb=" O GLU B 58 " pdb=" OE1 GLU B 58 " model vdw 2.560 3.040 nonbonded pdb=" O ASP A 131 " pdb=" OG1 THR A 217 " model vdw 2.574 3.040 nonbonded pdb=" SG CYS A 109 " pdb=" CB CYS A 126 " model vdw 2.600 3.040 ... (remaining 22064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 3.170 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.510 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2984 Z= 0.165 Angle : 0.861 7.333 4038 Z= 0.462 Chirality : 0.047 0.228 448 Planarity : 0.007 0.068 520 Dihedral : 13.480 85.429 1081 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.05 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.45), residues: 365 helix: 0.41 (0.42), residues: 164 sheet: -2.17 (1.46), residues: 12 loop : -2.21 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 121 TYR 0.025 0.003 TYR A 112 PHE 0.025 0.001 PHE A 67 TRP 0.007 0.001 TRP A 105 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2976) covalent geometry : angle 0.85422 ( 4032) hydrogen bonds : bond 0.15431 ( 125) hydrogen bonds : angle 5.21552 ( 360) metal coordination : bond 0.01695 ( 8) metal coordination : angle 2.87551 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7920 (mptt) cc_final: 0.7536 (mmtp) REVERT: B 25 GLN cc_start: 0.8269 (mp10) cc_final: 0.8057 (mp10) REVERT: B 28 THR cc_start: 0.8805 (m) cc_final: 0.8359 (t) REVERT: B 44 GLU cc_start: 0.7623 (tp30) cc_final: 0.7172 (tp30) REVERT: B 45 GLU cc_start: 0.7243 (tp30) cc_final: 0.6936 (tp30) REVERT: B 67 GLU cc_start: 0.8323 (pt0) cc_final: 0.7923 (pt0) REVERT: B 117 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 97 LYS cc_start: 0.8366 (mmpt) cc_final: 0.7967 (mmtm) REVERT: A 145 ASN cc_start: 0.8903 (p0) cc_final: 0.8651 (p0) REVERT: A 190 MET cc_start: 0.6544 (ttm) cc_final: 0.6065 (ttm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0530 time to fit residues: 7.7227 Evaluate side-chains 102 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.163413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.146913 restraints weight = 6631.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.150601 restraints weight = 4266.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153177 restraints weight = 2995.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.154954 restraints weight = 2211.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.156282 restraints weight = 1708.976| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2984 Z= 0.153 Angle : 0.749 8.940 4038 Z= 0.378 Chirality : 0.046 0.223 448 Planarity : 0.005 0.057 520 Dihedral : 5.490 21.539 406 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 1.10 % Allowed : 10.41 % Favored : 88.49 % Rotamer: Outliers : 3.21 % Allowed : 15.38 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.45), residues: 365 helix: 0.49 (0.42), residues: 158 sheet: -1.79 (1.54), residues: 12 loop : -2.10 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 121 TYR 0.023 0.002 TYR A 170 PHE 0.031 0.002 PHE A 149 TRP 0.009 0.001 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2976) covalent geometry : angle 0.74259 ( 4032) hydrogen bonds : bond 0.03884 ( 125) hydrogen bonds : angle 4.88430 ( 360) metal coordination : bond 0.00795 ( 8) metal coordination : angle 2.56897 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7755 (mptt) cc_final: 0.7433 (mmtp) REVERT: B 25 GLN cc_start: 0.8397 (mp10) cc_final: 0.8195 (mp10) REVERT: B 56 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 86 TYR cc_start: 0.8111 (t80) cc_final: 0.7351 (t80) REVERT: B 91 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8711 (ptpp) REVERT: A 44 SER cc_start: 0.6646 (p) cc_final: 0.6431 (p) REVERT: A 97 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8039 (mmtm) REVERT: A 113 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8280 (mtp85) REVERT: A 190 MET cc_start: 0.6611 (ttm) cc_final: 0.6088 (ttm) outliers start: 10 outliers final: 9 residues processed: 118 average time/residue: 0.0514 time to fit residues: 7.0062 Evaluate side-chains 112 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.162552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146032 restraints weight = 6711.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.149830 restraints weight = 4256.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.152508 restraints weight = 2937.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154311 restraints weight = 2133.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.155613 restraints weight = 1628.674| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2984 Z= 0.150 Angle : 0.739 9.588 4038 Z= 0.373 Chirality : 0.046 0.222 448 Planarity : 0.005 0.055 520 Dihedral : 5.462 21.059 406 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 1.10 % Allowed : 10.96 % Favored : 87.95 % Rotamer: Outliers : 4.49 % Allowed : 20.51 % Favored : 75.00 % 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 are not related in a simple way. whole: -1.47 (0.45), residues: 365 helix: 0.30 (0.41), residues: 164 sheet: -1.44 (1.66), residues: 12 loop : -2.18 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 215 TYR 0.016 0.002 TYR A 91 PHE 0.036 0.002 PHE B 30 TRP 0.008 0.001 TRP A 105 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2976) covalent geometry : angle 0.73234 ( 4032) hydrogen bonds : bond 0.03608 ( 125) hydrogen bonds : angle 4.79362 ( 360) metal coordination : bond 0.00923 ( 8) metal coordination : angle 2.58278 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7640 (mptt) cc_final: 0.7388 (mmtp) REVERT: B 25 GLN cc_start: 0.8473 (mp10) cc_final: 0.8210 (mp10) REVERT: B 86 TYR cc_start: 0.8260 (t80) cc_final: 0.7497 (t80) REVERT: A 44 SER cc_start: 0.6563 (p) cc_final: 0.6329 (p) REVERT: A 78 GLU cc_start: 0.8060 (mp0) cc_final: 0.7609 (mp0) REVERT: A 190 MET cc_start: 0.6554 (ttm) cc_final: 0.6064 (ttm) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.0607 time to fit residues: 8.1899 Evaluate side-chains 117 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 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 = 0.4233 r_free = 0.4233 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.145952 restraints weight = 6526.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149526 restraints weight = 4202.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152036 restraints weight = 2939.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.153760 restraints weight = 2167.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.155097 restraints weight = 1677.086| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2984 Z= 0.147 Angle : 0.741 9.843 4038 Z= 0.375 Chirality : 0.046 0.222 448 Planarity : 0.005 0.049 520 Dihedral : 5.405 20.265 406 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 1.10 % Allowed : 10.96 % Favored : 87.95 % Rotamer: Outliers : 4.17 % Allowed : 24.36 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.45), residues: 365 helix: 0.60 (0.42), residues: 158 sheet: -1.24 (1.72), residues: 12 loop : -2.29 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 143 TYR 0.013 0.002 TYR A 91 PHE 0.024 0.002 PHE B 30 TRP 0.017 0.002 TRP A 105 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2976) covalent geometry : angle 0.73617 ( 4032) hydrogen bonds : bond 0.03476 ( 125) hydrogen bonds : angle 4.78948 ( 360) metal coordination : bond 0.00810 ( 8) metal coordination : angle 2.41042 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7585 (mptt) cc_final: 0.7314 (mmtp) REVERT: B 25 GLN cc_start: 0.8475 (mp10) cc_final: 0.8211 (mp10) REVERT: B 56 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 86 TYR cc_start: 0.8339 (t80) cc_final: 0.7621 (t80) REVERT: B 91 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8641 (ptpp) REVERT: A 44 SER cc_start: 0.6515 (p) cc_final: 0.6277 (p) REVERT: A 103 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5265 (ptt) REVERT: A 143 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7154 (ptt90) REVERT: A 190 MET cc_start: 0.6565 (ttm) cc_final: 0.6080 (ttm) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.0602 time to fit residues: 7.9374 Evaluate side-chains 115 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.159340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143743 restraints weight = 6755.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.147187 restraints weight = 4356.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149580 restraints weight = 3053.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.151260 restraints weight = 2263.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.152390 restraints weight = 1750.706| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2984 Z= 0.182 Angle : 0.794 9.486 4038 Z= 0.399 Chirality : 0.047 0.221 448 Planarity : 0.005 0.048 520 Dihedral : 5.678 21.630 406 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.33 % Favored : 86.58 % Rotamer: Outliers : 5.13 % Allowed : 25.64 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.45), residues: 365 helix: 0.34 (0.41), residues: 164 sheet: -1.81 (1.48), residues: 12 loop : -2.21 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 118 TYR 0.018 0.002 TYR A 112 PHE 0.022 0.002 PHE B 30 TRP 0.013 0.002 TRP A 105 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 2976) covalent geometry : angle 0.78648 ( 4032) hydrogen bonds : bond 0.03551 ( 125) hydrogen bonds : angle 4.92854 ( 360) metal coordination : bond 0.01149 ( 8) metal coordination : angle 2.99184 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7702 (mptt) cc_final: 0.7334 (mmtp) REVERT: B 25 GLN cc_start: 0.8487 (mp10) cc_final: 0.8211 (mp10) REVERT: B 76 TYR cc_start: 0.8753 (m-80) cc_final: 0.8473 (m-80) REVERT: B 86 TYR cc_start: 0.8414 (t80) cc_final: 0.7713 (t80) REVERT: B 91 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8685 (ptpp) REVERT: A 78 GLU cc_start: 0.7985 (mp0) cc_final: 0.7562 (mp0) REVERT: A 190 MET cc_start: 0.6666 (ttm) cc_final: 0.6185 (ttm) outliers start: 16 outliers final: 9 residues processed: 112 average time/residue: 0.0546 time to fit residues: 7.0905 Evaluate side-chains 112 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.161154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145280 restraints weight = 6818.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.148835 restraints weight = 4356.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.151272 restraints weight = 3043.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.152913 restraints weight = 2249.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.154250 restraints weight = 1750.245| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2984 Z= 0.146 Angle : 0.776 10.771 4038 Z= 0.385 Chirality : 0.046 0.216 448 Planarity : 0.005 0.043 520 Dihedral : 5.521 20.435 406 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 1.10 % Allowed : 11.51 % Favored : 87.40 % Rotamer: Outliers : 3.21 % Allowed : 28.21 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.45), residues: 365 helix: 0.62 (0.41), residues: 158 sheet: -1.64 (1.55), residues: 12 loop : -2.31 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 121 TYR 0.017 0.002 TYR A 112 PHE 0.035 0.002 PHE B 30 TRP 0.012 0.002 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2976) covalent geometry : angle 0.77003 ( 4032) hydrogen bonds : bond 0.03221 ( 125) hydrogen bonds : angle 4.78239 ( 360) metal coordination : bond 0.00662 ( 8) metal coordination : angle 2.57474 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7729 (mptt) cc_final: 0.7362 (mmtp) REVERT: B 25 GLN cc_start: 0.8460 (mp10) cc_final: 0.8179 (mp10) REVERT: B 41 GLN cc_start: 0.8222 (mp10) cc_final: 0.7683 (pm20) REVERT: B 76 TYR cc_start: 0.8712 (m-80) cc_final: 0.8440 (m-80) REVERT: B 86 TYR cc_start: 0.8404 (t80) cc_final: 0.7684 (t80) REVERT: B 91 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8644 (ptpp) REVERT: A 78 GLU cc_start: 0.7937 (mp0) cc_final: 0.7487 (mp0) REVERT: A 113 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8188 (mtm180) REVERT: A 190 MET cc_start: 0.6568 (ttm) cc_final: 0.6065 (ttm) outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 0.0524 time to fit residues: 6.7157 Evaluate side-chains 113 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.160605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.144610 restraints weight = 6995.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148095 restraints weight = 4526.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150525 restraints weight = 3179.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.152259 restraints weight = 2351.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.153474 restraints weight = 1821.779| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2984 Z= 0.154 Angle : 0.767 10.133 4038 Z= 0.381 Chirality : 0.046 0.218 448 Planarity : 0.005 0.046 520 Dihedral : 5.557 20.434 406 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.51 % Favored : 87.67 % Rotamer: Outliers : 3.85 % Allowed : 29.81 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.45), residues: 365 helix: 0.68 (0.41), residues: 158 sheet: -1.40 (1.58), residues: 12 loop : -2.27 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 118 TYR 0.015 0.002 TYR B 96 PHE 0.027 0.001 PHE B 30 TRP 0.025 0.003 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2976) covalent geometry : angle 0.76194 ( 4032) hydrogen bonds : bond 0.03290 ( 125) hydrogen bonds : angle 4.79006 ( 360) metal coordination : bond 0.00652 ( 8) metal coordination : angle 2.39656 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7759 (mptt) cc_final: 0.7411 (mmmt) REVERT: B 25 GLN cc_start: 0.8397 (mp10) cc_final: 0.8165 (mp10) REVERT: B 41 GLN cc_start: 0.8184 (mp10) cc_final: 0.7681 (pm20) REVERT: B 86 TYR cc_start: 0.8419 (t80) cc_final: 0.7722 (t80) REVERT: B 91 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8638 (ptpp) REVERT: A 78 GLU cc_start: 0.7956 (mp0) cc_final: 0.7736 (mp0) REVERT: A 143 ARG cc_start: 0.8061 (ptt90) cc_final: 0.7483 (ptt90) REVERT: A 190 MET cc_start: 0.6584 (ttm) cc_final: 0.6089 (ttm) outliers start: 12 outliers final: 11 residues processed: 111 average time/residue: 0.0591 time to fit residues: 7.5344 Evaluate side-chains 113 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.160888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.144763 restraints weight = 7094.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148313 restraints weight = 4575.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.150740 restraints weight = 3198.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.152412 restraints weight = 2369.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153653 restraints weight = 1851.226| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2984 Z= 0.155 Angle : 0.781 10.267 4038 Z= 0.389 Chirality : 0.046 0.218 448 Planarity : 0.005 0.041 520 Dihedral : 5.604 20.865 406 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.82 % Allowed : 10.68 % Favored : 88.49 % Rotamer: Outliers : 4.81 % Allowed : 28.53 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.45), residues: 365 helix: 0.67 (0.42), residues: 158 sheet: -1.31 (1.52), residues: 12 loop : -2.26 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.011 0.001 TYR B 18 PHE 0.025 0.001 PHE B 30 TRP 0.019 0.002 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2976) covalent geometry : angle 0.77586 ( 4032) hydrogen bonds : bond 0.03250 ( 125) hydrogen bonds : angle 4.78622 ( 360) metal coordination : bond 0.00691 ( 8) metal coordination : angle 2.35678 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7749 (mptt) cc_final: 0.7365 (mmtp) REVERT: B 25 GLN cc_start: 0.8363 (mp10) cc_final: 0.8129 (mp10) REVERT: B 41 GLN cc_start: 0.8161 (mp10) cc_final: 0.7696 (pm20) REVERT: B 86 TYR cc_start: 0.8431 (t80) cc_final: 0.7752 (t80) REVERT: B 91 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8636 (ptpp) REVERT: A 97 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8372 (mmtm) REVERT: A 143 ARG cc_start: 0.8045 (ptt90) cc_final: 0.7418 (ptt90) REVERT: A 190 MET cc_start: 0.6568 (ttm) cc_final: 0.6078 (ttm) outliers start: 15 outliers final: 14 residues processed: 114 average time/residue: 0.0747 time to fit residues: 9.7157 Evaluate side-chains 116 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.161368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.145322 restraints weight = 6857.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148830 restraints weight = 4433.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.151260 restraints weight = 3082.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.152871 restraints weight = 2276.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154106 restraints weight = 1776.456| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2984 Z= 0.156 Angle : 0.797 10.417 4038 Z= 0.393 Chirality : 0.045 0.218 448 Planarity : 0.005 0.047 520 Dihedral : 5.629 20.891 406 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.51 % Favored : 87.67 % Rotamer: Outliers : 4.81 % Allowed : 28.21 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.45), residues: 365 helix: 0.69 (0.42), residues: 158 sheet: -1.01 (1.55), residues: 12 loop : -2.25 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 121 TYR 0.016 0.002 TYR B 18 PHE 0.025 0.001 PHE B 30 TRP 0.019 0.002 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2976) covalent geometry : angle 0.79275 ( 4032) hydrogen bonds : bond 0.03260 ( 125) hydrogen bonds : angle 4.75994 ( 360) metal coordination : bond 0.00794 ( 8) metal coordination : angle 2.21045 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7733 (mptt) cc_final: 0.7453 (mmmt) REVERT: B 25 GLN cc_start: 0.8344 (mp10) cc_final: 0.8129 (mp10) REVERT: B 41 GLN cc_start: 0.8161 (mp10) cc_final: 0.7691 (pm20) REVERT: B 86 TYR cc_start: 0.8421 (t80) cc_final: 0.7784 (t80) REVERT: B 91 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8622 (ptpp) REVERT: A 97 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8413 (mmtm) REVERT: A 113 ARG cc_start: 0.8401 (mtm180) cc_final: 0.8173 (ttp-110) REVERT: A 143 ARG cc_start: 0.8037 (ptt90) cc_final: 0.7668 (ptt90) REVERT: A 190 MET cc_start: 0.6532 (ttm) cc_final: 0.6043 (ttm) REVERT: A 232 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.4164 (p90) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.0722 time to fit residues: 9.2440 Evaluate side-chains 112 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.161772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145569 restraints weight = 6989.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.149052 restraints weight = 4551.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.151432 restraints weight = 3212.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.153124 restraints weight = 2385.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.154370 restraints weight = 1853.766| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2984 Z= 0.147 Angle : 0.803 10.846 4038 Z= 0.396 Chirality : 0.045 0.218 448 Planarity : 0.005 0.049 520 Dihedral : 5.506 20.515 406 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.78 % Favored : 87.40 % Rotamer: Outliers : 3.85 % Allowed : 29.49 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.46), residues: 365 helix: 0.77 (0.42), residues: 157 sheet: -0.67 (1.49), residues: 12 loop : -2.23 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 121 TYR 0.012 0.001 TYR B 18 PHE 0.024 0.001 PHE B 30 TRP 0.016 0.002 TRP A 105 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 2976) covalent geometry : angle 0.79994 ( 4032) hydrogen bonds : bond 0.03198 ( 125) hydrogen bonds : angle 4.70168 ( 360) metal coordination : bond 0.00514 ( 8) metal coordination : angle 2.00574 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7685 (mptt) cc_final: 0.7412 (mmmt) REVERT: B 25 GLN cc_start: 0.8333 (mp10) cc_final: 0.8123 (mp10) REVERT: B 41 GLN cc_start: 0.8206 (mp10) cc_final: 0.7724 (pm20) REVERT: B 86 TYR cc_start: 0.8440 (t80) cc_final: 0.7784 (t80) REVERT: B 91 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8607 (ptpp) REVERT: A 97 LYS cc_start: 0.8676 (mmpt) cc_final: 0.8416 (mmtm) REVERT: A 113 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7493 (ttp-110) REVERT: A 143 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7479 (ptt90) REVERT: A 190 MET cc_start: 0.6534 (ttm) cc_final: 0.6020 (ttm) REVERT: A 232 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.4129 (p90) outliers start: 12 outliers final: 11 residues processed: 112 average time/residue: 0.0792 time to fit residues: 10.1227 Evaluate side-chains 110 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0010 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.161363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.145096 restraints weight = 6953.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.148585 restraints weight = 4543.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150987 restraints weight = 3187.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152685 restraints weight = 2374.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.153854 restraints weight = 1845.027| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2984 Z= 0.151 Angle : 0.798 10.738 4038 Z= 0.395 Chirality : 0.046 0.220 448 Planarity : 0.005 0.047 520 Dihedral : 5.520 20.819 406 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.82 % Allowed : 10.96 % Favored : 88.22 % Rotamer: Outliers : 4.17 % Allowed : 29.81 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.46), residues: 365 helix: 0.75 (0.42), residues: 158 sheet: -0.42 (1.55), residues: 12 loop : -2.19 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 118 TYR 0.012 0.002 TYR B 18 PHE 0.024 0.001 PHE B 30 TRP 0.016 0.002 TRP A 105 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2976) covalent geometry : angle 0.79489 ( 4032) hydrogen bonds : bond 0.03393 ( 125) hydrogen bonds : angle 4.69050 ( 360) metal coordination : bond 0.00582 ( 8) metal coordination : angle 2.01612 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 658.64 seconds wall clock time: 12 minutes 0.94 seconds (720.94 seconds total)