Starting phenix.real_space_refine on Tue Aug 4 16:28:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.map" model { file = "/net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rjb_54010/08_2026/9rjb_54010.cif" } resolution = 2.6 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= 0.019 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 21 5.16 5 C 3149 2.51 5 N 786 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4784 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1349 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "A" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1404 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "D" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 524 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "E" Number of atoms: 190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 20, 155 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Conformer: "B" Number of residues, atoms: 20, 155 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} bond proxies already assigned to first conformer: 120 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ASER E 20 " occ=0.70 ... (10 atoms not shown) pdb=" OG BSER E 20 " occ=0.30 residue: pdb=" N AALA E 21 " occ=0.70 ... (8 atoms not shown) pdb=" CB BALA E 21 " occ=0.30 residue: pdb=" N ATYR E 22 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR E 22 " occ=0.30 residue: pdb=" N AALA E 23 " occ=0.70 ... (8 atoms not shown) pdb=" CB BALA E 23 " occ=0.30 residue: pdb=" N APRO E 24 " occ=0.70 ... (12 atoms not shown) pdb=" CD BPRO E 24 " occ=0.30 Time building chain proxies: 1.40, per 1000 atoms: 0.29 Number of scatterers: 4784 At special positions: 0 Unit cell: (116.8, 77.38, 73, 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 21 16.00 O 828 8.00 N 786 7.00 C 3149 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: 0.43 Conformation dependent library (CDL) restraints added in 210.9 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 43.3% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 51 through 71 Processing helix chain 'C' and resid 77 through 104 Processing helix chain 'C' and resid 105 through 134 Proline residue: C 111 - end of helix removed outlier: 3.803A pdb=" N LEU C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 219 removed outlier: 3.536A pdb=" N TYR C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.669A pdb=" N ARG A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 44 Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'D' and resid 3 through 31 removed outlier: 4.285A pdb=" N THR D 30 " --> pdb=" O CYS D 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 110 Processing helix chain 'B' and resid 112 through 131 Processing helix chain 'E' and resid 6 through 17 Processing sheet with id=AA1, first strand: chain 'C' and resid 74 through 75 removed outlier: 5.855A pdb=" N ILE C 138 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER C 160 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 70 current: chain 'A' and resid 94 through 103 removed outlier: 5.212A pdb=" N VAL A 98 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS A 114 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 100 " --> pdb=" O LEU A 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 133 through 134 current: chain 'D' and resid 100 through 111 Processing sheet with id=AA3, first strand: chain 'D' and resid 40 through 50 removed outlier: 5.392A pdb=" N LEU D 41 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR D 71 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL D 43 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP D 69 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 45 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE D 66 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS D 124 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N PHE D 68 " --> pdb=" O ASP D 122 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 684 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: 0.68 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 915 1.33 - 1.45: 1183 1.45 - 1.57: 2764 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4899 Sorted by residual: bond pdb=" CE1 HIS C 143 " pdb=" NE2 HIS C 143 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.41e+01 bond pdb=" N ASP D 62 " pdb=" CA ASP D 62 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.22e-02 6.72e+03 1.04e+01 bond pdb=" C VAL E 18 " pdb=" N PRO E 19 " ideal model delta sigma weight residual 1.329 1.361 -0.033 1.20e-02 6.94e+03 7.41e+00 bond pdb=" N ASER E 20 " pdb=" CA ASER E 20 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.15e-02 7.56e+03 7.35e+00 bond pdb=" N VAL A 73 " pdb=" CA VAL A 73 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.24e+00 ... (remaining 4894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6387 1.63 - 3.26: 204 3.26 - 4.88: 36 4.88 - 6.51: 3 6.51 - 8.14: 1 Bond angle restraints: 6631 Sorted by residual: angle pdb=" N BPRO E 24 " pdb=" CA BPRO E 24 " pdb=" CB BPRO E 24 " ideal model delta sigma weight residual 103.00 94.86 8.14 1.10e+00 8.26e-01 5.47e+01 angle pdb=" CA BTYR E 22 " pdb=" C BTYR E 22 " pdb=" O BTYR E 22 " ideal model delta sigma weight residual 120.51 114.01 6.50 1.43e+00 4.89e-01 2.07e+01 angle pdb=" O BTYR E 22 " pdb=" C BTYR E 22 " pdb=" N BALA E 23 " ideal model delta sigma weight residual 122.59 127.81 -5.22 1.33e+00 5.65e-01 1.54e+01 angle pdb=" N VAL C 122 " pdb=" CA VAL C 122 " pdb=" C VAL C 122 " ideal model delta sigma weight residual 110.53 107.27 3.26 9.40e-01 1.13e+00 1.20e+01 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 114.48 110.71 3.77 1.19e+00 7.06e-01 1.00e+01 ... (remaining 6626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 2646 17.07 - 34.14: 202 34.14 - 51.21: 38 51.21 - 68.28: 4 68.28 - 85.35: 3 Dihedral angle restraints: 2893 sinusoidal: 1164 harmonic: 1729 Sorted by residual: dihedral pdb=" CD ARG A 72 " pdb=" NE ARG A 72 " pdb=" CZ ARG A 72 " pdb=" NH1 ARG A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -85.35 85.35 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CD ARG D 60 " pdb=" NE ARG D 60 " pdb=" CZ ARG D 60 " pdb=" NH1 ARG D 60 " ideal model delta sinusoidal sigma weight residual 0.00 84.89 -84.89 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CA LYS D 33 " pdb=" C LYS D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 625 0.057 - 0.113: 113 0.113 - 0.170: 15 0.170 - 0.227: 1 0.227 - 0.283: 2 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA VAL D 51 " pdb=" N VAL D 51 " pdb=" C VAL D 51 " pdb=" CB VAL D 51 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA BTYR E 22 " pdb=" N BTYR E 22 " pdb=" C BTYR E 22 " pdb=" CB BTYR E 22 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU B 145 " pdb=" N LEU B 145 " pdb=" C LEU B 145 " pdb=" CB LEU B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.58e-01 ... (remaining 753 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 72 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 72 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 72 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 72 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 72 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 60 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG D 60 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 60 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 60 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER E 20 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C BSER E 20 " -0.054 2.00e-02 2.50e+03 pdb=" O BSER E 20 " 0.020 2.00e-02 2.50e+03 pdb=" N BALA E 21 " 0.019 2.00e-02 2.50e+03 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 6 2.44 - 3.06: 2928 3.06 - 3.67: 6917 3.67 - 4.29: 10569 4.29 - 4.90: 17810 Nonbonded interactions: 38230 Sorted by model distance: nonbonded pdb=" CD LYS D 33 " pdb=" OD2 ASP D 79 " model vdw 1.827 3.440 nonbonded pdb=" OD1 ASP D 62 " pdb=" CD1 LEU D 136 " model vdw 2.335 3.460 nonbonded pdb=" NZ LYS C 56 " pdb=" OG SER C 160 " model vdw 2.388 3.120 nonbonded pdb=" O TYR C 133 " pdb=" NZ LYS C 136 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP C 101 " pdb=" NZ LYS A 37 " model vdw 2.418 3.120 ... (remaining 38225 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=0.30 max=1.00 mean=0.99 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: 4.220 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 0.040 4899 Z= 0.272 Angle : 0.619 8.138 6631 Z= 0.403 Chirality : 0.046 0.283 756 Planarity : 0.025 0.493 815 Dihedral : 12.566 85.355 1773 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.38 % Allowed : 1.71 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.27 (0.36), residues: 576 helix: 3.13 (0.31), residues: 218 sheet: 0.54 (0.45), residues: 139 loop : -1.44 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.004 0.001 TYR A 126 PHE 0.011 0.001 PHE B 91 TRP 0.016 0.001 TRP D 80 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.27 ( 4899) covalent geometry : angle 0.61867 / 0.40 ( 6631) hydrogen bonds : bond 0.19005 / 12.90 ( 232) hydrogen bonds : angle 6.13736 / 4.33 ( 684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: C 124 MET cc_start: 0.8217 (mmm) cc_final: 0.7986 (mmp) REVERT: A 104 LYS cc_start: 0.7384 (mttt) cc_final: 0.7155 (mttm) REVERT: D 3 THR cc_start: 0.8356 (p) cc_final: 0.8122 (t) REVERT: D 60 ARG cc_start: 0.5595 (tpt170) cc_final: 0.4773 (tmm160) REVERT: B 114 TRP cc_start: 0.6601 (m100) cc_final: 0.6103 (m-10) REVERT: B 138 ARG cc_start: 0.7331 (mtm180) cc_final: 0.5904 (mmt180) REVERT: E 6 LYS cc_start: 0.8411 (mttt) cc_final: 0.6617 (tptp) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.5584 time to fit residues: 78.0246 Evaluate side-chains 83 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 HIS C 198 HIS A 21 GLN D 42 HIS D 101 ASN D 149 ASN B 140 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129345 restraints weight = 21836.531| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.51 r_work: 0.3437 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4899 Z= 0.140 Angle : 0.535 10.386 6631 Z= 0.274 Chirality : 0.042 0.143 756 Planarity : 0.004 0.047 815 Dihedral : 3.576 12.669 635 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.61 % Allowed : 10.08 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.52 (0.35), residues: 576 helix: 3.27 (0.30), residues: 225 sheet: 0.72 (0.46), residues: 124 loop : -1.28 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 7 TYR 0.008 0.001 TYR A 20 PHE 0.017 0.001 PHE B 91 TRP 0.010 0.001 TRP D 80 HIS 0.008 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4899) covalent geometry : angle 0.53546 / 0.27 ( 6631) hydrogen bonds : bond 0.05138 / 3.33 ( 232) hydrogen bonds : angle 4.30260 / 3.08 ( 684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.117 Fit side-chains REVERT: C 72 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7469 (mmmt) REVERT: C 113 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 11 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: A 72 ARG cc_start: 0.7955 (mtp85) cc_final: 0.6611 (mtt-85) REVERT: D 60 ARG cc_start: 0.6830 (tpt170) cc_final: 0.5214 (tmm160) REVERT: B 114 TRP cc_start: 0.6838 (m100) cc_final: 0.6045 (m-10) REVERT: B 138 ARG cc_start: 0.7698 (mtm180) cc_final: 0.5939 (mmt180) outliers start: 18 outliers final: 3 residues processed: 98 average time/residue: 0.5416 time to fit residues: 55.0769 Evaluate side-chains 82 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain D residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 157 GLN C 198 HIS A 157 ASN D 98 ASN B 140 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130373 restraints weight = 14179.184| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.74 r_work: 0.3482 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4899 Z= 0.116 Angle : 0.519 10.450 6631 Z= 0.258 Chirality : 0.041 0.137 756 Planarity : 0.004 0.040 815 Dihedral : 3.554 14.306 635 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.23 % Allowed : 12.74 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.63 (0.36), residues: 576 helix: 3.36 (0.31), residues: 225 sheet: 0.83 (0.48), residues: 116 loop : -1.17 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.007 0.001 TYR A 20 PHE 0.015 0.001 PHE B 91 TRP 0.010 0.001 TRP D 80 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4899) covalent geometry : angle 0.51860 / 0.26 ( 6631) hydrogen bonds : bond 0.04516 / 2.93 ( 232) hydrogen bonds : angle 4.04249 / 2.92 ( 684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.152 Fit side-chains REVERT: C 129 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (mp) REVERT: C 213 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.6874 (tmm160) REVERT: A 11 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8011 (mtp85) REVERT: A 72 ARG cc_start: 0.7905 (mtp85) cc_final: 0.6549 (mtt-85) REVERT: D 60 ARG cc_start: 0.6895 (tpt170) cc_final: 0.5246 (tmm160) REVERT: B 114 TRP cc_start: 0.6802 (m100) cc_final: 0.6024 (m-10) REVERT: B 138 ARG cc_start: 0.7707 (mtm180) cc_final: 0.5882 (mmt180) outliers start: 17 outliers final: 6 residues processed: 90 average time/residue: 0.4970 time to fit residues: 46.4699 Evaluate side-chains 85 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain B residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS D 101 ASN B 140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126392 restraints weight = 15876.746| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.93 r_work: 0.3426 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4899 Z= 0.159 Angle : 0.561 10.411 6631 Z= 0.282 Chirality : 0.043 0.138 756 Planarity : 0.003 0.031 815 Dihedral : 3.952 13.132 635 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.99 % Allowed : 14.45 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.37 (0.35), residues: 576 helix: 3.08 (0.32), residues: 225 sheet: 0.74 (0.47), residues: 116 loop : -1.28 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.009 0.001 TYR A 20 PHE 0.018 0.001 PHE B 91 TRP 0.014 0.001 TRP D 80 HIS 0.003 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 4899) covalent geometry : angle 0.56135 / 0.28 ( 6631) hydrogen bonds : bond 0.04866 / 3.13 ( 232) hydrogen bonds : angle 4.16102 / 3.00 ( 684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.131 Fit side-chains REVERT: C 98 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7741 (tp) REVERT: C 129 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7411 (mp) REVERT: C 213 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.6845 (tmm160) REVERT: A 72 ARG cc_start: 0.7983 (mtp85) cc_final: 0.6589 (mtt-85) REVERT: D 47 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8061 (ttt) REVERT: D 60 ARG cc_start: 0.7160 (tpt170) cc_final: 0.5228 (tmm160) REVERT: B 114 TRP cc_start: 0.7043 (m100) cc_final: 0.6124 (m-10) REVERT: B 138 ARG cc_start: 0.7824 (mtm180) cc_final: 0.5963 (mmt180) outliers start: 21 outliers final: 7 residues processed: 91 average time/residue: 0.4870 time to fit residues: 45.9768 Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain B residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 GLN C 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129128 restraints weight = 10778.730| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.35 r_work: 0.3477 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4899 Z= 0.123 Angle : 0.524 10.454 6631 Z= 0.262 Chirality : 0.041 0.138 756 Planarity : 0.003 0.032 815 Dihedral : 3.706 12.100 635 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.04 % Allowed : 16.54 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.43 (0.35), residues: 576 helix: 3.11 (0.32), residues: 226 sheet: 0.79 (0.47), residues: 115 loop : -1.25 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.007 0.001 TYR A 20 PHE 0.015 0.001 PHE B 91 TRP 0.009 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4899) covalent geometry : angle 0.52402 / 0.26 ( 6631) hydrogen bonds : bond 0.04414 / 2.84 ( 232) hydrogen bonds : angle 4.01342 / 2.91 ( 684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.182 Fit side-chains REVERT: C 113 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (mp) REVERT: C 129 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7377 (mp) REVERT: C 204 MET cc_start: 0.8342 (mmm) cc_final: 0.8123 (tpp) REVERT: C 213 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.6811 (tmm160) REVERT: A 72 ARG cc_start: 0.7940 (mtp85) cc_final: 0.6601 (mtt-85) REVERT: D 23 THR cc_start: 0.8392 (m) cc_final: 0.8159 (m) REVERT: D 47 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: D 60 ARG cc_start: 0.7021 (tpt170) cc_final: 0.5122 (tmm160) REVERT: D 75 GLU cc_start: 0.6967 (pm20) cc_final: 0.6751 (pm20) REVERT: B 114 TRP cc_start: 0.6946 (m100) cc_final: 0.6071 (m-10) REVERT: B 138 ARG cc_start: 0.7745 (mtm180) cc_final: 0.5872 (mmt180) outliers start: 16 outliers final: 4 residues processed: 87 average time/residue: 0.5459 time to fit residues: 49.2080 Evaluate side-chains 82 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain B residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127958 restraints weight = 12453.654| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.53 r_work: 0.3457 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4899 Z= 0.129 Angle : 0.532 10.435 6631 Z= 0.266 Chirality : 0.041 0.138 756 Planarity : 0.003 0.031 815 Dihedral : 3.723 12.027 635 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.42 % Allowed : 16.54 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.42 (0.35), residues: 576 helix: 3.13 (0.32), residues: 225 sheet: 0.77 (0.47), residues: 115 loop : -1.26 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.008 0.001 TYR A 20 PHE 0.016 0.001 PHE B 91 TRP 0.010 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4899) covalent geometry : angle 0.53204 / 0.27 ( 6631) hydrogen bonds : bond 0.04461 / 2.88 ( 232) hydrogen bonds : angle 4.01568 / 2.91 ( 684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.199 Fit side-chains REVERT: C 98 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7653 (tp) REVERT: C 129 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 213 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6841 (tmm160) REVERT: A 72 ARG cc_start: 0.7965 (mtp85) cc_final: 0.6619 (mtt-85) REVERT: D 23 THR cc_start: 0.8439 (m) cc_final: 0.8234 (m) REVERT: D 47 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8019 (ttt) REVERT: D 60 ARG cc_start: 0.7121 (tpt170) cc_final: 0.5084 (ttt180) REVERT: D 75 GLU cc_start: 0.6972 (pm20) cc_final: 0.6741 (pm20) REVERT: B 114 TRP cc_start: 0.7002 (m100) cc_final: 0.6077 (m-10) REVERT: B 138 ARG cc_start: 0.7759 (mtm180) cc_final: 0.5879 (mmt180) outliers start: 18 outliers final: 7 residues processed: 87 average time/residue: 0.5304 time to fit residues: 47.9464 Evaluate side-chains 85 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS D 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125443 restraints weight = 13064.884| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.80 r_work: 0.3405 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4899 Z= 0.154 Angle : 0.560 10.351 6631 Z= 0.280 Chirality : 0.042 0.138 756 Planarity : 0.003 0.032 815 Dihedral : 3.892 12.545 635 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.18 % Allowed : 15.21 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.33 (0.35), residues: 576 helix: 3.01 (0.32), residues: 225 sheet: 0.72 (0.47), residues: 115 loop : -1.26 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.009 0.001 TYR A 20 PHE 0.019 0.001 PHE B 91 TRP 0.012 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 4899) covalent geometry : angle 0.55956 / 0.28 ( 6631) hydrogen bonds : bond 0.04717 / 3.02 ( 232) hydrogen bonds : angle 4.10360 / 2.97 ( 684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.200 Fit side-chains REVERT: C 98 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7694 (tp) REVERT: C 113 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 129 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7298 (mp) REVERT: C 213 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6755 (tmm160) REVERT: A 72 ARG cc_start: 0.7990 (mtp85) cc_final: 0.6591 (mtt-85) REVERT: D 47 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8084 (ttt) REVERT: D 60 ARG cc_start: 0.7178 (tpt170) cc_final: 0.4955 (ttt180) REVERT: D 122 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: D 140 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7238 (mmt180) REVERT: B 114 TRP cc_start: 0.6899 (m100) cc_final: 0.5990 (m-10) REVERT: B 138 ARG cc_start: 0.7765 (mtm180) cc_final: 0.5814 (mmt180) outliers start: 22 outliers final: 10 residues processed: 87 average time/residue: 0.5759 time to fit residues: 52.0927 Evaluate side-chains 89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain B residue 91 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.126624 restraints weight = 17269.101| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.03 r_work: 0.3427 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4899 Z= 0.124 Angle : 0.522 7.690 6631 Z= 0.262 Chirality : 0.041 0.136 756 Planarity : 0.003 0.032 815 Dihedral : 3.885 26.338 635 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 17.11 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.38 (0.35), residues: 576 helix: 3.13 (0.32), residues: 225 sheet: 0.70 (0.47), residues: 115 loop : -1.28 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 139 TYR 0.008 0.001 TYR A 20 PHE 0.018 0.001 PHE B 91 TRP 0.009 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4899) covalent geometry : angle 0.52214 / 0.26 ( 6631) hydrogen bonds : bond 0.04381 / 2.81 ( 232) hydrogen bonds : angle 3.98596 / 2.90 ( 684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.198 Fit side-chains REVERT: C 113 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7691 (mp) REVERT: C 129 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7388 (mp) REVERT: C 213 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6877 (tmm160) REVERT: A 72 ARG cc_start: 0.7968 (mtp85) cc_final: 0.6588 (mtt-85) REVERT: D 47 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8070 (ttt) REVERT: D 60 ARG cc_start: 0.7303 (tpt170) cc_final: 0.5013 (ttt180) REVERT: D 140 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7318 (mmt180) REVERT: B 114 TRP cc_start: 0.6955 (m100) cc_final: 0.6070 (m-10) REVERT: B 138 ARG cc_start: 0.7820 (mtm180) cc_final: 0.5902 (mmt180) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.5774 time to fit residues: 49.8294 Evaluate side-chains 83 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain B residue 91 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS A 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128387 restraints weight = 10173.617| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.46 r_work: 0.3451 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4899 Z= 0.130 Angle : 0.525 7.692 6631 Z= 0.263 Chirality : 0.041 0.139 756 Planarity : 0.003 0.032 815 Dihedral : 3.885 23.190 635 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.85 % Allowed : 16.92 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.37 (0.36), residues: 576 helix: 3.13 (0.32), residues: 225 sheet: 0.68 (0.47), residues: 115 loop : -1.29 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.008 0.001 TYR A 20 PHE 0.019 0.001 PHE B 91 TRP 0.010 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4899) covalent geometry : angle 0.52490 / 0.26 ( 6631) hydrogen bonds : bond 0.04438 / 2.85 ( 232) hydrogen bonds : angle 3.99160 / 2.89 ( 684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.182 Fit side-chains REVERT: C 98 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7689 (tp) REVERT: C 113 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7655 (mp) REVERT: C 129 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7260 (mp) REVERT: C 204 MET cc_start: 0.8377 (mmm) cc_final: 0.8109 (tpp) REVERT: C 213 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6811 (tmm160) REVERT: A 72 ARG cc_start: 0.7952 (mtp85) cc_final: 0.6575 (mtt-85) REVERT: D 47 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8041 (ttt) REVERT: D 60 ARG cc_start: 0.7219 (tpt170) cc_final: 0.5011 (ttt180) REVERT: D 140 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7246 (mmt180) REVERT: B 114 TRP cc_start: 0.6870 (m100) cc_final: 0.5989 (m-10) REVERT: B 138 ARG cc_start: 0.7775 (mtm180) cc_final: 0.5791 (mmt180) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.5783 time to fit residues: 48.0738 Evaluate side-chains 84 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain B residue 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS A 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127790 restraints weight = 12081.064| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.55 r_work: 0.3431 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4899 Z= 0.117 Angle : 0.513 7.843 6631 Z= 0.257 Chirality : 0.041 0.137 756 Planarity : 0.003 0.032 815 Dihedral : 3.774 20.768 635 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.85 % Allowed : 17.11 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.42 (0.36), residues: 576 helix: 3.18 (0.32), residues: 225 sheet: 0.71 (0.47), residues: 115 loop : -1.29 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.007 0.001 TYR A 20 PHE 0.018 0.001 PHE B 91 TRP 0.009 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4899) covalent geometry : angle 0.51251 / 0.26 ( 6631) hydrogen bonds : bond 0.04282 / 2.75 ( 232) hydrogen bonds : angle 3.93329 / 2.86 ( 684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.188 Fit side-chains REVERT: C 129 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7244 (mp) REVERT: C 213 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6744 (tmm160) REVERT: A 72 ARG cc_start: 0.7932 (mtp85) cc_final: 0.6567 (mtt-85) REVERT: D 47 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7994 (ttt) REVERT: D 60 ARG cc_start: 0.7184 (tpt170) cc_final: 0.4939 (ttt180) REVERT: D 140 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7268 (mmt180) REVERT: B 114 TRP cc_start: 0.6811 (m100) cc_final: 0.5891 (m-10) REVERT: B 138 ARG cc_start: 0.7776 (mtm180) cc_final: 0.5785 (mmt180) outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 0.5429 time to fit residues: 47.4503 Evaluate side-chains 81 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 HIS A 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126656 restraints weight = 12124.043| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.55 r_work: 0.3418 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4899 Z= 0.139 Angle : 0.538 7.861 6631 Z= 0.271 Chirality : 0.042 0.137 756 Planarity : 0.003 0.032 815 Dihedral : 3.927 20.058 635 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 17.49 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.24 (0.36), residues: 576 helix: 3.07 (0.32), residues: 225 sheet: 0.39 (0.45), residues: 125 loop : -1.35 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 139 TYR 0.018 0.001 TYR C 71 PHE 0.021 0.001 PHE B 91 TRP 0.015 0.001 TRP D 80 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4899) covalent geometry : angle 0.53794 / 0.27 ( 6631) hydrogen bonds : bond 0.04521 / 2.91 ( 232) hydrogen bonds : angle 4.01476 / 2.91 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.03 seconds wall clock time: 36 minutes 10.53 seconds (2170.53 seconds total)