Starting phenix.real_space_refine on Tue Aug 4 12:27:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.cif Found real_map, /net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.map" model { file = "/net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/35tl_77181/08_2026/35tl_77181.cif" } resolution = 3.93 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= 0.023 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 13 5.16 5 C 1671 2.51 5 N 441 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s 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: 2620 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "B" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 0.72, per 1000 atoms: 0.27 Number of scatterers: 2620 At special positions: 0 Unit cell: (55.86, 68.6, 84.28, 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 13 16.00 O 495 8.00 N 441 7.00 C 1671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.30 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 57.7 milliseconds 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 6.6% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.662A pdb=" N ARG A 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 removed outlier: 3.812A pdb=" N MET B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 100 through 107 Proline residue: B 105 - end of helix Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.825A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.220A pdb=" N TYR A 11 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 38 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN A 49 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TRP A 40 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.849A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 81 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 22 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.743A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 94 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 116 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 57 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.517A pdb=" N ILE C 75 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 21 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 48 removed outlier: 7.220A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 34 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 92 " --> pdb=" O GLY C 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 44 through 48 removed outlier: 7.220A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 34 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 86 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.32 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 834 1.35 - 1.47: 594 1.47 - 1.59: 1228 1.59 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 2676 Sorted by residual: bond pdb=" N ILE C 106 " pdb=" CA ILE C 106 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" N ASP A 73 " pdb=" CA ASP A 73 " ideal model delta sigma weight residual 1.452 1.491 -0.038 1.22e-02 6.72e+03 9.77e+00 bond pdb=" N VAL C 58 " pdb=" CA VAL C 58 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.01e-02 9.80e+03 9.50e+00 bond pdb=" N VAL A 27 " pdb=" CA VAL A 27 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.24e-02 6.50e+03 9.48e+00 bond pdb=" N ILE A 21 " pdb=" CA ILE A 21 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.41e+00 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 3171 1.55 - 3.09: 364 3.09 - 4.64: 77 4.64 - 6.18: 8 6.18 - 7.73: 4 Bond angle restraints: 3624 Sorted by residual: angle pdb=" CA GLU B 89 " pdb=" CB GLU B 89 " pdb=" CG GLU B 89 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA GLY C 95 " pdb=" C GLY C 95 " pdb=" O GLY C 95 " ideal model delta sigma weight residual 122.78 118.36 4.42 1.20e+00 6.94e-01 1.36e+01 angle pdb=" CA ILE C 106 " pdb=" C ILE C 106 " pdb=" O ILE C 106 " ideal model delta sigma weight residual 121.67 117.99 3.68 1.02e+00 9.61e-01 1.30e+01 angle pdb=" CA ILE A 109 " pdb=" CB ILE A 109 " pdb=" CG1 ILE A 109 " ideal model delta sigma weight residual 110.40 116.38 -5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CA VAL A 87 " pdb=" C VAL A 87 " pdb=" O VAL A 87 " ideal model delta sigma weight residual 121.70 117.99 3.71 1.06e+00 8.90e-01 1.23e+01 ... (remaining 3619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 1393 16.39 - 32.78: 131 32.78 - 49.17: 46 49.17 - 65.56: 17 65.56 - 81.95: 3 Dihedral angle restraints: 1590 sinusoidal: 626 harmonic: 964 Sorted by residual: dihedral pdb=" CB GLU B 6 " pdb=" CG GLU B 6 " pdb=" CD GLU B 6 " pdb=" OE1 GLU B 6 " ideal model delta sinusoidal sigma weight residual 0.00 81.95 -81.95 1 3.00e+01 1.11e-03 9.17e+00 dihedral pdb=" CG ARG A 67 " pdb=" CD ARG A 67 " pdb=" NE ARG A 67 " pdb=" CZ ARG A 67 " ideal model delta sinusoidal sigma weight residual 180.00 140.20 39.80 2 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" CG ARG B 59 " pdb=" CD ARG B 59 " pdb=" NE ARG B 59 " pdb=" CZ ARG B 59 " ideal model delta sinusoidal sigma weight residual -90.00 -50.28 -39.72 2 1.50e+01 4.44e-03 8.71e+00 ... (remaining 1587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 288 0.077 - 0.154: 95 0.154 - 0.231: 16 0.231 - 0.308: 1 0.308 - 0.385: 1 Chirality restraints: 401 Sorted by residual: chirality pdb=" CB THR C 20 " pdb=" CA THR C 20 " pdb=" OG1 THR C 20 " pdb=" CG2 THR C 20 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 398 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 13 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO B 14 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.191 9.50e-02 1.11e+02 8.63e-02 5.55e+00 pdb=" NE ARG B 59 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 39 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO C 40 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " -0.027 5.00e-02 4.00e+02 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1016 2.92 - 3.41: 2031 3.41 - 3.91: 3889 3.91 - 4.40: 3870 4.40 - 4.90: 6993 Nonbonded interactions: 17799 Sorted by model distance: nonbonded pdb=" O ASN A 79 " pdb=" OD1 ASN A 79 " model vdw 2.420 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" O GLN A 90 " model vdw 2.450 3.040 nonbonded pdb=" O ALA A 34 " pdb=" ND1 HIS A 52 " model vdw 2.570 3.120 nonbonded pdb=" OE2 GLU A 54 " pdb=" OE1 GLU A 55 " model vdw 2.587 3.040 nonbonded pdb=" N ASN A 46 " pdb=" OD1 ASN A 46 " model vdw 2.594 3.120 ... (remaining 17794 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: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.010 Process input model: 4.080 Find NCS groups from input model: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 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 : 0.010 0.268 2679 Z= 0.633 Angle : 1.171 24.174 3630 Z= 0.745 Chirality : 0.074 0.385 401 Planarity : 0.008 0.086 458 Dihedral : 15.740 81.950 969 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.44), residues: 328 helix: None (None), residues: 0 sheet: -0.27 (0.50), residues: 120 loop : -2.56 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 59 TYR 0.027 0.002 TYR A 39 PHE 0.007 0.001 PHE C 53 TRP 0.014 0.002 TRP B 97 HIS 0.006 0.002 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.58 ( 2676) covalent geometry : angle 1.08979 / 0.72 ( 3624) SS BOND : bond 0.15480 / 7.37 ( 3) SS BOND : angle 10.59619 / 10.13 ( 6) hydrogen bonds : bond 0.33126 / 21.51 ( 59) hydrogen bonds : angle 10.13650 / 6.83 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.062 Fit side-chains REVERT: A 96 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7097 (mtm-85) REVERT: B 47 TRP cc_start: 0.8117 (t60) cc_final: 0.7708 (t60) REVERT: B 50 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8202 (ttp80) REVERT: C 31 LYS cc_start: 0.7301 (mmtp) cc_final: 0.6734 (mttt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0546 time to fit residues: 4.4086 Evaluate side-chains 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0060 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164991 restraints weight = 4172.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167448 restraints weight = 2838.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169236 restraints weight = 2138.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170516 restraints weight = 1715.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.171452 restraints weight = 1429.823| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2679 Z= 0.112 Angle : 0.567 7.251 3630 Z= 0.298 Chirality : 0.044 0.143 401 Planarity : 0.004 0.047 458 Dihedral : 4.315 12.555 367 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.47 % Allowed : 23.32 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.45), residues: 328 helix: None (None), residues: 0 sheet: -0.49 (0.48), residues: 130 loop : -2.34 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.012 0.001 TYR C 50 PHE 0.010 0.001 PHE C 53 TRP 0.011 0.001 TRP B 97 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 2676) covalent geometry : angle 0.56541 / 0.30 ( 3624) SS BOND : bond 0.00499 / 0.26 ( 3) SS BOND : angle 1.10706 / 0.80 ( 6) hydrogen bonds : bond 0.03839 / 2.49 ( 59) hydrogen bonds : angle 6.08665 / 4.20 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.098 Fit side-chains REVERT: A 96 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7316 (mtm-85) REVERT: B 47 TRP cc_start: 0.8245 (t60) cc_final: 0.7876 (t60) REVERT: B 50 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8257 (ttp80) REVERT: C 31 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6701 (mtmt) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.0609 time to fit residues: 4.5547 Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.0170 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161229 restraints weight = 4274.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.163615 restraints weight = 2948.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165360 restraints weight = 2241.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166424 restraints weight = 1805.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167176 restraints weight = 1548.849| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2679 Z= 0.124 Angle : 0.582 5.488 3630 Z= 0.303 Chirality : 0.045 0.139 401 Planarity : 0.004 0.046 458 Dihedral : 4.292 12.800 367 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.89 % Allowed : 22.61 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.45), residues: 328 helix: None (None), residues: 0 sheet: -0.56 (0.45), residues: 136 loop : -2.23 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 59 TYR 0.023 0.001 TYR C 49 PHE 0.013 0.002 PHE C 53 TRP 0.012 0.001 TRP B 97 HIS 0.001 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 2676) covalent geometry : angle 0.58010 / 0.30 ( 3624) SS BOND : bond 0.00593 / 0.31 ( 3) SS BOND : angle 1.27572 / 0.86 ( 6) hydrogen bonds : bond 0.03668 / 2.31 ( 59) hydrogen bonds : angle 5.46229 / 3.71 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.106 Fit side-chains REVERT: B 50 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8229 (ttp80) REVERT: B 82 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5439 (tt0) REVERT: C 12 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7464 (t) REVERT: C 50 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.4437 (m-80) outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 0.0787 time to fit residues: 5.9336 Evaluate side-chains 58 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.178780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160495 restraints weight = 4456.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162687 restraints weight = 3121.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164304 restraints weight = 2388.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165620 restraints weight = 1948.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166524 restraints weight = 1662.877| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2679 Z= 0.124 Angle : 0.603 10.546 3630 Z= 0.303 Chirality : 0.045 0.142 401 Planarity : 0.004 0.046 458 Dihedral : 4.307 12.674 367 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.18 % Allowed : 25.09 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.50 (0.44), residues: 139 loop : -2.12 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.022 0.001 TYR C 49 PHE 0.011 0.001 PHE C 53 TRP 0.012 0.002 TRP B 97 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 2676) covalent geometry : angle 0.60214 / 0.30 ( 3624) SS BOND : bond 0.00580 / 0.30 ( 3) SS BOND : angle 1.11057 / 0.73 ( 6) hydrogen bonds : bond 0.03312 / 2.12 ( 59) hydrogen bonds : angle 5.18570 / 3.52 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5916 (pp) REVERT: B 50 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8128 (ttp80) REVERT: B 82 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.5337 (tt0) REVERT: C 36 TYR cc_start: 0.6923 (m-80) cc_final: 0.6122 (m-80) REVERT: C 50 TYR cc_start: 0.5962 (OUTLIER) cc_final: 0.4246 (m-80) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 0.0786 time to fit residues: 5.4097 Evaluate side-chains 57 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155295 restraints weight = 4506.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157635 restraints weight = 3198.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159415 restraints weight = 2452.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160667 restraints weight = 2005.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161458 restraints weight = 1710.320| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2679 Z= 0.135 Angle : 0.608 8.181 3630 Z= 0.308 Chirality : 0.045 0.147 401 Planarity : 0.004 0.046 458 Dihedral : 4.421 13.504 367 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.95 % Allowed : 23.67 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.50 (0.44), residues: 137 loop : -2.19 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.021 0.001 TYR C 49 PHE 0.011 0.002 PHE C 53 TRP 0.013 0.002 TRP B 97 HIS 0.001 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 2676) covalent geometry : angle 0.60650 / 0.31 ( 3624) SS BOND : bond 0.00584 / 0.31 ( 3) SS BOND : angle 1.14957 / 0.75 ( 6) hydrogen bonds : bond 0.03407 / 2.20 ( 59) hydrogen bonds : angle 5.25008 / 3.56 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: B 11 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5982 (pp) REVERT: B 50 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8196 (ttp80) REVERT: B 82 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5167 (tt0) REVERT: C 50 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4297 (m-80) outliers start: 14 outliers final: 5 residues processed: 62 average time/residue: 0.0836 time to fit residues: 5.9888 Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 90 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 17 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.179632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.161196 restraints weight = 4428.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163570 restraints weight = 3080.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.165412 restraints weight = 2344.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166595 restraints weight = 1895.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167541 restraints weight = 1613.766| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2679 Z= 0.098 Angle : 0.557 7.272 3630 Z= 0.280 Chirality : 0.045 0.150 401 Planarity : 0.004 0.043 458 Dihedral : 4.087 12.766 367 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.53 % Allowed : 27.21 % Favored : 69.26 % 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: -1.88 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.18 (0.44), residues: 135 loop : -2.15 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.017 0.001 TYR C 49 PHE 0.006 0.001 PHE C 53 TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 2676) covalent geometry : angle 0.55700 / 0.28 ( 3624) SS BOND : bond 0.00412 / 0.22 ( 3) SS BOND : angle 0.75587 / 0.53 ( 6) hydrogen bonds : bond 0.02901 / 1.89 ( 59) hydrogen bonds : angle 4.89310 / 3.28 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6632 (tt0) REVERT: B 11 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6029 (pp) REVERT: B 50 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8092 (ttp80) REVERT: C 36 TYR cc_start: 0.6773 (m-80) cc_final: 0.5995 (m-80) REVERT: C 50 TYR cc_start: 0.5903 (OUTLIER) cc_final: 0.4189 (m-80) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.0858 time to fit residues: 5.6356 Evaluate side-chains 56 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.169973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150445 restraints weight = 4350.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152791 restraints weight = 3071.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154601 restraints weight = 2356.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.155803 restraints weight = 1938.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156646 restraints weight = 1665.864| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2679 Z= 0.151 Angle : 0.647 8.293 3630 Z= 0.327 Chirality : 0.046 0.149 401 Planarity : 0.004 0.044 458 Dihedral : 4.479 13.850 367 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.89 % Allowed : 27.56 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.50 (0.43), residues: 138 loop : -2.20 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 59 TYR 0.019 0.002 TYR C 49 PHE 0.015 0.002 PHE C 53 TRP 0.014 0.002 TRP B 97 HIS 0.002 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 2676) covalent geometry : angle 0.64579 / 0.33 ( 3624) SS BOND : bond 0.00560 / 0.29 ( 3) SS BOND : angle 1.13620 / 0.73 ( 6) hydrogen bonds : bond 0.03397 / 2.17 ( 59) hydrogen bonds : angle 5.18391 / 3.44 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7530 (p90) cc_final: 0.7273 (p90) REVERT: A 55 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: A 66 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: B 11 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6036 (pp) REVERT: C 50 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4165 (m-80) REVERT: C 54 LEU cc_start: 0.7493 (pp) cc_final: 0.7265 (pp) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.0636 time to fit residues: 4.4382 Evaluate side-chains 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 90 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.176260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157342 restraints weight = 4404.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159721 restraints weight = 3098.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161504 restraints weight = 2366.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162734 restraints weight = 1932.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163645 restraints weight = 1646.547| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2679 Z= 0.119 Angle : 0.617 7.430 3630 Z= 0.308 Chirality : 0.045 0.154 401 Planarity : 0.004 0.044 458 Dihedral : 4.244 12.705 367 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.59 % Allowed : 27.56 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.40 (0.43), residues: 137 loop : -2.14 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.016 0.001 TYR C 49 PHE 0.008 0.001 PHE C 53 TRP 0.010 0.001 TRP B 97 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2676) covalent geometry : angle 0.61618 / 0.31 ( 3624) SS BOND : bond 0.00453 / 0.24 ( 3) SS BOND : angle 0.89517 / 0.60 ( 6) hydrogen bonds : bond 0.03078 / 1.97 ( 59) hydrogen bonds : angle 4.88048 / 3.20 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7545 (p90) cc_final: 0.7280 (p90) REVERT: A 55 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: A 66 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: B 11 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5953 (pp) REVERT: C 50 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.4200 (m-80) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.0769 time to fit residues: 5.3056 Evaluate side-chains 60 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 90 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0010 chunk 23 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.157894 restraints weight = 4533.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160239 restraints weight = 3219.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161846 restraints weight = 2485.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163102 restraints weight = 2028.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164093 restraints weight = 1726.671| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2679 Z= 0.129 Angle : 0.617 7.531 3630 Z= 0.313 Chirality : 0.046 0.157 401 Planarity : 0.004 0.043 458 Dihedral : 4.330 13.316 367 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.30 % Allowed : 26.86 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.46), residues: 328 helix: None (None), residues: 0 sheet: -0.39 (0.43), residues: 137 loop : -2.15 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 18 TYR 0.017 0.001 TYR C 49 PHE 0.010 0.001 PHE C 53 TRP 0.011 0.001 TRP B 97 HIS 0.001 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 2676) covalent geometry : angle 0.61603 / 0.31 ( 3624) SS BOND : bond 0.00500 / 0.26 ( 3) SS BOND : angle 0.97607 / 0.63 ( 6) hydrogen bonds : bond 0.03167 / 2.04 ( 59) hydrogen bonds : angle 4.91842 / 3.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7626 (p90) cc_final: 0.7336 (p90) REVERT: A 55 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: A 66 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6675 (tt0) REVERT: B 11 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.5957 (pp) REVERT: C 50 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.4080 (m-80) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.0817 time to fit residues: 5.8360 Evaluate side-chains 59 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 90 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.152569 restraints weight = 4527.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154925 restraints weight = 3207.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156775 restraints weight = 2474.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157968 restraints weight = 2024.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158881 restraints weight = 1736.382| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2679 Z= 0.132 Angle : 0.641 8.603 3630 Z= 0.322 Chirality : 0.046 0.164 401 Planarity : 0.004 0.043 458 Dihedral : 4.369 14.431 367 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.24 % Allowed : 27.56 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.45), residues: 328 helix: None (None), residues: 0 sheet: -0.39 (0.43), residues: 135 loop : -2.15 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 18 TYR 0.016 0.001 TYR C 49 PHE 0.010 0.001 PHE C 53 TRP 0.011 0.001 TRP B 97 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 2676) covalent geometry : angle 0.64016 / 0.32 ( 3624) SS BOND : bond 0.00487 / 0.25 ( 3) SS BOND : angle 0.95090 / 0.63 ( 6) hydrogen bonds : bond 0.03218 / 2.07 ( 59) hydrogen bonds : angle 4.91373 / 3.21 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 656 Ramachandran restraints generated. 328 Oldfield, 0 Emsley, 328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7636 (p90) cc_final: 0.7362 (p90) REVERT: A 55 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: B 11 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5939 (pp) REVERT: C 50 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.4078 (m-80) REVERT: C 52 LYS cc_start: 0.8406 (tptt) cc_final: 0.7109 (pttt) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.0708 time to fit residues: 5.0219 Evaluate side-chains 56 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0010 chunk 14 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.171717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152378 restraints weight = 4422.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154679 restraints weight = 3165.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156351 restraints weight = 2452.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157527 restraints weight = 2032.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158533 restraints weight = 1753.411| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2679 Z= 0.135 Angle : 0.665 10.562 3630 Z= 0.328 Chirality : 0.046 0.197 401 Planarity : 0.004 0.043 458 Dihedral : 4.442 16.396 367 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.53 % Allowed : 28.98 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.45), residues: 328 helix: None (None), residues: 0 sheet: -0.39 (0.43), residues: 135 loop : -2.14 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.017 0.001 TYR C 49 PHE 0.009 0.001 PHE C 53 TRP 0.016 0.002 TRP B 47 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 2676) covalent geometry : angle 0.66428 / 0.33 ( 3624) SS BOND : bond 0.00512 / 0.27 ( 3) SS BOND : angle 0.99278 / 0.64 ( 6) hydrogen bonds : bond 0.03180 / 2.05 ( 59) hydrogen bonds : angle 4.88573 / 3.20 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 740.53 seconds wall clock time: 13 minutes 22.85 seconds (802.85 seconds total)