Starting phenix.real_space_refine on Fri Aug 22 17:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq5_17105/08_2025/8oq5_17105.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4128 2.51 5 N 1044 2.21 5 O 1320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6528 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Restraints were copied for chains: B, C, D, E, F, G, H, I, L, M, N Time building chain proxies: 0.91, per 1000 atoms: 0.14 Number of scatterers: 6528 At special positions: 0 Unit cell: (117.52, 91.52, 49.92, 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 36 16.00 O 1320 8.00 N 1044 7.00 C 4128 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: 0.40 Conformation dependent library (CDL) restraints added in 214.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.681A pdb=" N ASP A 6 " --> pdb=" O MET C 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP C 6 " --> pdb=" O MET E 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP E 6 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP G 6 " --> pdb=" O MET I 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP I 6 " --> pdb=" O MET M 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.252A pdb=" N LEU A 10 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 10 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 10 " --> pdb=" O PHE G 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU G 10 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU I 10 " --> pdb=" O PHE M 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.092A pdb=" N THR A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR I 19 " --> pdb=" O GLU M 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49 removed outlier: 8.747A pdb=" N GLU A 47 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU C 47 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU E 47 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU G 47 " --> pdb=" O GLN I 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU I 47 " --> pdb=" O GLN M 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.681A pdb=" N ASP B 6 " --> pdb=" O MET D 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP D 6 " --> pdb=" O MET F 7 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP F 6 " --> pdb=" O MET H 7 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP H 6 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP L 6 " --> pdb=" O MET N 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.251A pdb=" N LEU B 10 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 10 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 10 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 10 " --> pdb=" O PHE L 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU L 10 " --> pdb=" O PHE N 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 21 removed outlier: 6.093A pdb=" N THR B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR H 19 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR L 19 " --> pdb=" O GLU N 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB3, first strand: chain 'B' and resid 46 through 49 removed outlier: 8.746A pdb=" N GLU B 47 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU D 47 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLU F 47 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLU H 47 " --> pdb=" O GLN L 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU L 47 " --> pdb=" O GLN N 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 64 70 hydrogen bonds defined for protein. 210 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: 0.74 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1116 1.29 - 1.42: 1659 1.42 - 1.56: 3764 1.56 - 1.69: 25 1.69 - 1.82: 72 Bond restraints: 6636 Sorted by residual: bond pdb=" C TYR I 21 " pdb=" O TYR I 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.45e+01 bond pdb=" C TYR N 21 " pdb=" O TYR N 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.45e+01 bond pdb=" C TYR F 21 " pdb=" O TYR F 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.44e+01 bond pdb=" C TYR H 21 " pdb=" O TYR H 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.44e+01 bond pdb=" C TYR C 21 " pdb=" O TYR C 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.43e+01 ... (remaining 6631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 5714 1.72 - 3.43: 2295 3.43 - 5.15: 706 5.15 - 6.86: 177 6.86 - 8.58: 12 Bond angle restraints: 8904 Sorted by residual: angle pdb=" N ILE H 34 " pdb=" CA ILE H 34 " pdb=" C ILE H 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE G 34 " pdb=" CA ILE G 34 " pdb=" C ILE G 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE I 34 " pdb=" CA ILE I 34 " pdb=" C ILE I 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE D 34 " pdb=" CA ILE D 34 " pdb=" C ILE D 34 " ideal model delta sigma weight residual 107.37 115.94 -8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" N ILE N 34 " pdb=" CA ILE N 34 " pdb=" C ILE N 34 " ideal model delta sigma weight residual 107.37 115.93 -8.56 1.48e+00 4.57e-01 3.35e+01 ... (remaining 8899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.61: 3252 9.61 - 19.22: 384 19.22 - 28.84: 204 28.84 - 38.45: 96 38.45 - 48.06: 84 Dihedral angle restraints: 4020 sinusoidal: 1620 harmonic: 2400 Sorted by residual: dihedral pdb=" CA ALA L 40 " pdb=" C ALA L 40 " pdb=" N TYR L 41 " pdb=" CA TYR L 41 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA B 40 " pdb=" C ALA B 40 " pdb=" N TYR B 41 " pdb=" CA TYR B 41 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N TYR C 41 " pdb=" CA TYR C 41 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 312 0.047 - 0.094: 288 0.094 - 0.141: 237 0.141 - 0.187: 87 0.187 - 0.234: 60 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA VAL D 61 " pdb=" N VAL D 61 " pdb=" C VAL D 61 " pdb=" CB VAL D 61 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL L 61 " pdb=" N VAL L 61 " pdb=" C VAL L 61 " pdb=" CB VAL L 61 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL F 61 " pdb=" N VAL F 61 " pdb=" C VAL F 61 " pdb=" CB VAL F 61 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 981 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 16 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN I 16 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN I 16 " -0.021 2.00e-02 2.50e+03 pdb=" N SER I 17 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 67 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU N 67 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU N 67 " 0.021 2.00e-02 2.50e+03 pdb=" N MET N 68 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 16 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C GLN G 16 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN G 16 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 17 " -0.020 2.00e-02 2.50e+03 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 3421 2.99 - 3.47: 5989 3.47 - 3.95: 11952 3.95 - 4.42: 13817 4.42 - 4.90: 25285 Nonbonded interactions: 60464 Sorted by model distance: nonbonded pdb=" OG SER B 66 " pdb=" O PHE D 63 " model vdw 2.517 3.040 nonbonded pdb=" OG SER H 66 " pdb=" O PHE L 63 " model vdw 2.517 3.040 nonbonded pdb=" OG SER C 66 " pdb=" O PHE E 63 " model vdw 2.518 3.040 nonbonded pdb=" OG SER E 66 " pdb=" O PHE G 63 " model vdw 2.518 3.040 nonbonded pdb=" OG SER F 66 " pdb=" O PHE H 63 " model vdw 2.518 3.040 ... (remaining 60459 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.015 0.069 6636 Z= 1.137 Angle : 2.049 8.581 8904 Z= 1.453 Chirality : 0.100 0.234 984 Planarity : 0.011 0.033 1140 Dihedral : 14.254 48.059 2460 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.16), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.12), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 54 TYR 0.031 0.006 TYR L 21 PHE 0.016 0.005 PHE I 11 HIS 0.002 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.01548 ( 6636) covalent geometry : angle 2.04919 ( 8904) hydrogen bonds : bond 0.19575 ( 70) hydrogen bonds : angle 8.89849 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.177 Fit side-chains REVERT: N 50 THR cc_start: 0.8229 (p) cc_final: 0.8028 (p) outliers start: 0 outliers final: 3 residues processed: 313 average time/residue: 0.5735 time to fit residues: 187.7447 Evaluate side-chains 242 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain N residue 6 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 35 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 13 GLN H 35 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 35 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 35 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 35 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114978 restraints weight = 7596.077| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.48 r_work: 0.3605 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6636 Z= 0.190 Angle : 0.709 7.824 8904 Z= 0.360 Chirality : 0.045 0.132 984 Planarity : 0.005 0.058 1140 Dihedral : 6.712 24.519 858 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.83 % Allowed : 15.85 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.33 (0.20), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.15), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 54 TYR 0.015 0.002 TYR G 21 PHE 0.011 0.002 PHE E 11 HIS 0.003 0.001 HIS E 46 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 6636) covalent geometry : angle 0.70898 ( 8904) hydrogen bonds : bond 0.03047 ( 70) hydrogen bonds : angle 5.17833 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 0.353 Fit side-chains REVERT: B 28 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8521 (mmtp) REVERT: B 41 TYR cc_start: 0.8751 (m-80) cc_final: 0.8424 (m-80) REVERT: E 24 ASP cc_start: 0.8319 (m-30) cc_final: 0.8108 (m-30) REVERT: G 30 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8578 (mtpt) REVERT: G 71 GLU cc_start: 0.7672 (tt0) cc_final: 0.7412 (mt-10) REVERT: H 71 GLU cc_start: 0.7382 (tt0) cc_final: 0.7171 (mt-10) REVERT: M 18 MET cc_start: 0.9102 (ttm) cc_final: 0.8817 (ttp) REVERT: M 25 LEU cc_start: 0.8337 (tt) cc_final: 0.8045 (tt) REVERT: M 37 GLN cc_start: 0.8473 (pt0) cc_final: 0.8256 (pt0) REVERT: N 6 ASP cc_start: 0.8840 (m-30) cc_final: 0.8626 (m-30) outliers start: 28 outliers final: 4 residues processed: 290 average time/residue: 0.5546 time to fit residues: 168.6417 Evaluate side-chains 248 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 243 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.115855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106897 restraints weight = 7600.013| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.43 r_work: 0.3503 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6636 Z= 0.243 Angle : 0.759 6.565 8904 Z= 0.383 Chirality : 0.047 0.171 984 Planarity : 0.005 0.058 1140 Dihedral : 6.745 24.684 852 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.87 % Allowed : 18.99 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG H 54 TYR 0.015 0.002 TYR G 21 PHE 0.012 0.002 PHE I 42 HIS 0.003 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 6636) covalent geometry : angle 0.75934 ( 8904) hydrogen bonds : bond 0.02575 ( 70) hydrogen bonds : angle 4.93959 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.292 Fit side-chains REVERT: A 70 LEU cc_start: 0.9347 (tt) cc_final: 0.9136 (tp) REVERT: B 41 TYR cc_start: 0.8754 (m-80) cc_final: 0.8512 (m-80) REVERT: C 33 GLU cc_start: 0.8023 (tt0) cc_final: 0.7630 (tm-30) REVERT: E 24 ASP cc_start: 0.8614 (m-30) cc_final: 0.8396 (m-30) REVERT: F 28 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: H 71 GLU cc_start: 0.7500 (tt0) cc_final: 0.7200 (mt-10) REVERT: M 18 MET cc_start: 0.9098 (ttm) cc_final: 0.8826 (ttp) REVERT: M 67 LEU cc_start: 0.8154 (mp) cc_final: 0.7929 (mp) REVERT: N 6 ASP cc_start: 0.8954 (m-30) cc_final: 0.8738 (m-30) outliers start: 21 outliers final: 9 residues processed: 264 average time/residue: 0.5827 time to fit residues: 160.5420 Evaluate side-chains 252 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107691 restraints weight = 7523.277| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.43 r_work: 0.3528 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6636 Z= 0.178 Angle : 0.683 7.424 8904 Z= 0.344 Chirality : 0.044 0.131 984 Planarity : 0.005 0.049 1140 Dihedral : 6.267 22.631 852 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.01 % Allowed : 22.81 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 54 TYR 0.013 0.002 TYR H 41 PHE 0.008 0.001 PHE N 42 HIS 0.002 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6636) covalent geometry : angle 0.68335 ( 8904) hydrogen bonds : bond 0.01957 ( 70) hydrogen bonds : angle 4.48554 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.205 Fit side-chains REVERT: B 41 TYR cc_start: 0.8691 (m-80) cc_final: 0.8450 (m-80) REVERT: C 33 GLU cc_start: 0.7977 (tt0) cc_final: 0.7559 (tm-30) REVERT: E 24 ASP cc_start: 0.8628 (m-30) cc_final: 0.8373 (m-30) REVERT: F 28 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8355 (mptt) REVERT: G 71 GLU cc_start: 0.7690 (tt0) cc_final: 0.7096 (mt-10) REVERT: H 9 SER cc_start: 0.8847 (p) cc_final: 0.8627 (m) REVERT: M 18 MET cc_start: 0.9098 (ttm) cc_final: 0.8848 (ttp) REVERT: M 37 GLN cc_start: 0.8669 (pt0) cc_final: 0.8451 (pt0) REVERT: N 6 ASP cc_start: 0.8980 (m-30) cc_final: 0.8713 (m-30) outliers start: 22 outliers final: 7 residues processed: 258 average time/residue: 0.5621 time to fit residues: 151.3032 Evaluate side-chains 250 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 242 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.113174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104167 restraints weight = 7502.335| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.38 r_work: 0.3452 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 6636 Z= 0.311 Angle : 0.801 8.965 8904 Z= 0.409 Chirality : 0.047 0.142 984 Planarity : 0.006 0.073 1140 Dihedral : 6.777 24.434 852 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.14 % Allowed : 23.63 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 54 TYR 0.013 0.003 TYR G 14 PHE 0.010 0.002 PHE N 42 HIS 0.004 0.002 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00727 ( 6636) covalent geometry : angle 0.80090 ( 8904) hydrogen bonds : bond 0.02474 ( 70) hydrogen bonds : angle 4.66136 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.201 Fit side-chains REVERT: A 43 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: B 41 TYR cc_start: 0.8684 (m-80) cc_final: 0.8394 (m-80) REVERT: C 33 GLU cc_start: 0.7994 (tt0) cc_final: 0.7640 (tm-30) REVERT: E 24 ASP cc_start: 0.8711 (m-30) cc_final: 0.8509 (m-30) REVERT: F 28 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8333 (mptt) REVERT: G 71 GLU cc_start: 0.7716 (tt0) cc_final: 0.7227 (mt-10) REVERT: M 27 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7814 (mm-30) REVERT: N 6 ASP cc_start: 0.9007 (m-30) cc_final: 0.8726 (m-30) REVERT: N 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8251 (m-80) outliers start: 23 outliers final: 13 residues processed: 252 average time/residue: 0.6063 time to fit residues: 159.3417 Evaluate side-chains 255 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 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 = 0.3760 r_free = 0.3760 target = 0.114957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105898 restraints weight = 7496.714| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.43 r_work: 0.3508 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6636 Z= 0.202 Angle : 0.708 8.179 8904 Z= 0.358 Chirality : 0.044 0.132 984 Planarity : 0.005 0.052 1140 Dihedral : 6.298 22.413 852 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.60 % Allowed : 25.00 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.58 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 54 TYR 0.013 0.002 TYR H 41 PHE 0.008 0.001 PHE E 11 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6636) covalent geometry : angle 0.70801 ( 8904) hydrogen bonds : bond 0.02037 ( 70) hydrogen bonds : angle 4.39208 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.272 Fit side-chains REVERT: B 41 TYR cc_start: 0.8664 (m-80) cc_final: 0.8430 (m-80) REVERT: C 33 GLU cc_start: 0.7993 (tt0) cc_final: 0.7614 (tm-30) REVERT: E 24 ASP cc_start: 0.8678 (m-30) cc_final: 0.8449 (m-30) REVERT: F 28 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8353 (mptt) REVERT: G 71 GLU cc_start: 0.7742 (tt0) cc_final: 0.7175 (mt-10) REVERT: N 6 ASP cc_start: 0.9012 (m-30) cc_final: 0.8738 (m-30) REVERT: N 41 TYR cc_start: 0.8487 (m-80) cc_final: 0.8180 (m-80) outliers start: 19 outliers final: 10 residues processed: 252 average time/residue: 0.6264 time to fit residues: 164.8349 Evaluate side-chains 251 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105373 restraints weight = 7308.517| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.36 r_work: 0.3476 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6636 Z= 0.274 Angle : 0.774 8.914 8904 Z= 0.394 Chirality : 0.046 0.141 984 Planarity : 0.006 0.066 1140 Dihedral : 6.575 23.680 852 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.05 % Allowed : 26.50 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 54 TYR 0.014 0.002 TYR G 14 PHE 0.009 0.002 PHE E 11 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 6636) covalent geometry : angle 0.77409 ( 8904) hydrogen bonds : bond 0.02323 ( 70) hydrogen bonds : angle 4.55459 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.281 Fit side-chains REVERT: B 41 TYR cc_start: 0.8666 (m-80) cc_final: 0.8376 (m-80) REVERT: C 33 GLU cc_start: 0.7961 (tt0) cc_final: 0.7594 (tm-30) REVERT: E 24 ASP cc_start: 0.8696 (m-30) cc_final: 0.8485 (m-30) REVERT: F 28 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8331 (mptt) REVERT: G 71 GLU cc_start: 0.7750 (tt0) cc_final: 0.7222 (mt-10) REVERT: I 71 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7492 (mt-10) REVERT: N 6 ASP cc_start: 0.9023 (m-30) cc_final: 0.8822 (m-30) REVERT: N 41 TYR cc_start: 0.8499 (m-80) cc_final: 0.8193 (m-80) REVERT: N 50 THR cc_start: 0.9068 (m) cc_final: 0.8864 (p) outliers start: 15 outliers final: 11 residues processed: 250 average time/residue: 0.6495 time to fit residues: 169.3637 Evaluate side-chains 250 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107647 restraints weight = 7520.854| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.41 r_work: 0.3535 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6636 Z= 0.168 Angle : 0.691 9.183 8904 Z= 0.347 Chirality : 0.043 0.130 984 Planarity : 0.005 0.050 1140 Dihedral : 6.042 21.002 852 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 26.64 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 54 TYR 0.014 0.002 TYR M 41 PHE 0.008 0.001 PHE E 11 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6636) covalent geometry : angle 0.69126 ( 8904) hydrogen bonds : bond 0.01856 ( 70) hydrogen bonds : angle 4.33928 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.292 Fit side-chains REVERT: B 41 TYR cc_start: 0.8638 (m-80) cc_final: 0.8389 (m-80) REVERT: C 33 GLU cc_start: 0.7959 (tt0) cc_final: 0.7586 (tm-30) REVERT: E 24 ASP cc_start: 0.8654 (m-30) cc_final: 0.8410 (m-30) REVERT: F 28 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: G 71 GLU cc_start: 0.7719 (tt0) cc_final: 0.7232 (mt-10) REVERT: I 43 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: I 71 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7497 (mt-10) REVERT: M 71 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7779 (mt-10) REVERT: N 6 ASP cc_start: 0.9002 (m-30) cc_final: 0.8738 (m-30) REVERT: N 41 TYR cc_start: 0.8467 (m-80) cc_final: 0.8245 (m-80) REVERT: N 50 THR cc_start: 0.8930 (m) cc_final: 0.8559 (p) outliers start: 17 outliers final: 11 residues processed: 257 average time/residue: 0.6027 time to fit residues: 161.9190 Evaluate side-chains 257 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 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 = 0.3765 r_free = 0.3765 target = 0.115362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.106181 restraints weight = 7621.652| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.42 r_work: 0.3517 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6636 Z= 0.195 Angle : 0.720 8.910 8904 Z= 0.361 Chirality : 0.045 0.135 984 Planarity : 0.005 0.053 1140 Dihedral : 6.135 21.045 852 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.91 % Allowed : 26.91 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 54 TYR 0.013 0.002 TYR M 41 PHE 0.010 0.001 PHE B 11 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6636) covalent geometry : angle 0.71956 ( 8904) hydrogen bonds : bond 0.01949 ( 70) hydrogen bonds : angle 4.41221 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.227 Fit side-chains REVERT: B 41 TYR cc_start: 0.8662 (m-80) cc_final: 0.8419 (m-80) REVERT: C 33 GLU cc_start: 0.7962 (tt0) cc_final: 0.7660 (tm-30) REVERT: E 24 ASP cc_start: 0.8671 (m-30) cc_final: 0.8403 (m-30) REVERT: F 28 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8401 (mptt) REVERT: G 71 GLU cc_start: 0.7761 (tt0) cc_final: 0.7268 (mt-10) REVERT: I 43 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: I 71 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7517 (mt-10) REVERT: N 6 ASP cc_start: 0.9017 (m-30) cc_final: 0.8744 (m-30) REVERT: N 41 TYR cc_start: 0.8470 (m-80) cc_final: 0.8232 (m-80) REVERT: N 50 THR cc_start: 0.8997 (m) cc_final: 0.8583 (p) outliers start: 14 outliers final: 11 residues processed: 248 average time/residue: 0.6261 time to fit residues: 161.9780 Evaluate side-chains 253 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 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 = 0.3790 r_free = 0.3790 target = 0.116670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107541 restraints weight = 7377.410| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.40 r_work: 0.3529 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6636 Z= 0.173 Angle : 0.703 9.019 8904 Z= 0.352 Chirality : 0.044 0.131 984 Planarity : 0.005 0.051 1140 Dihedral : 6.018 20.560 852 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.46 % Allowed : 27.46 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 54 TYR 0.014 0.002 TYR M 41 PHE 0.010 0.001 PHE B 11 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6636) covalent geometry : angle 0.70302 ( 8904) hydrogen bonds : bond 0.01806 ( 70) hydrogen bonds : angle 4.35890 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.201 Fit side-chains REVERT: C 33 GLU cc_start: 0.7959 (tt0) cc_final: 0.7646 (tm-30) REVERT: C 47 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7695 (mt-10) REVERT: E 24 ASP cc_start: 0.8666 (m-30) cc_final: 0.8393 (m-30) REVERT: F 9 SER cc_start: 0.9012 (p) cc_final: 0.8698 (m) REVERT: F 28 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8370 (mptt) REVERT: G 71 GLU cc_start: 0.7778 (tt0) cc_final: 0.7254 (mt-10) REVERT: I 43 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: I 71 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7588 (mt-10) REVERT: M 71 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7735 (mt-10) REVERT: N 6 ASP cc_start: 0.9005 (m-30) cc_final: 0.8743 (m-30) REVERT: N 41 TYR cc_start: 0.8469 (m-80) cc_final: 0.8217 (m-80) REVERT: N 50 THR cc_start: 0.8973 (m) cc_final: 0.8638 (p) outliers start: 18 outliers final: 12 residues processed: 253 average time/residue: 0.6204 time to fit residues: 163.8672 Evaluate side-chains 256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 13 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN L 13 GLN M 13 GLN N 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107375 restraints weight = 7378.343| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.39 r_work: 0.3537 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6636 Z= 0.174 Angle : 0.704 9.033 8904 Z= 0.352 Chirality : 0.044 0.132 984 Planarity : 0.005 0.051 1140 Dihedral : 5.993 20.486 852 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.91 % Allowed : 27.73 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 54 TYR 0.014 0.002 TYR M 41 PHE 0.011 0.001 PHE B 11 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6636) covalent geometry : angle 0.70389 ( 8904) hydrogen bonds : bond 0.01816 ( 70) hydrogen bonds : angle 4.36984 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.42 seconds wall clock time: 58 minutes 6.13 seconds (3486.13 seconds total)