Starting phenix.real_space_refine on Tue Mar 11 17:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq5_17105/03_2025/8oq5_17105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq5_17105/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq5_17105/03_2025/8oq5_17105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq5_17105/03_2025/8oq5_17105.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq5_17105/03_2025/8oq5_17105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq5_17105/03_2025/8oq5_17105.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F, I, H, M, L, N Time building chain proxies: 2.75, per 1000 atoms: 0.42 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: 1.55 Conformation dependent library (CDL) restraints added in 884.2 milliseconds 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: 0.97 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: 1.59 Time building geometry restraints manager: 1.84 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'M' selection = chain 'L' 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.540 Find NCS groups from input model: 0.150 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- 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= 1.005 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS B 46 PHE 0.016 0.005 PHE I 11 TYR 0.031 0.006 TYR L 21 ARG 0.001 0.000 ARG M 54 *********************** 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 : 0.643 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: 1.2200 time to fit residues: 399.2759 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 : 0.782 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 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 = 0.3934 r_free = 0.3934 target = 0.130516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120812 restraints weight = 7522.972| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.48 r_work: 0.3699 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6636 Z= 0.219 Angle : 0.658 8.540 8904 Z= 0.331 Chirality : 0.043 0.122 984 Planarity : 0.004 0.046 1140 Dihedral : 6.355 23.263 858 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.55 % Allowed : 18.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.20), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.15), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 46 PHE 0.009 0.001 PHE E 11 TYR 0.016 0.002 TYR G 21 ARG 0.004 0.002 ARG L 54 *********************** 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 296 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.816 Fit side-chains REVERT: A 69 ASN cc_start: 0.8323 (t0) cc_final: 0.8097 (t0) REVERT: B 28 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7980 (mptt) REVERT: G 30 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8503 (mtpt) REVERT: I 71 GLU cc_start: 0.7028 (tt0) cc_final: 0.6666 (mt-10) REVERT: M 30 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8398 (mtpt) REVERT: N 53 VAL cc_start: 0.9007 (p) cc_final: 0.8803 (p) outliers start: 26 outliers final: 4 residues processed: 284 average time/residue: 1.1041 time to fit residues: 329.1463 Evaluate side-chains 244 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS 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 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.0030 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 2 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.3855 r_free = 0.3855 target = 0.122920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113943 restraints weight = 7579.741| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.42 r_work: 0.3623 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6636 Z= 0.198 Angle : 0.666 8.473 8904 Z= 0.327 Chirality : 0.043 0.129 984 Planarity : 0.004 0.042 1140 Dihedral : 5.949 20.141 852 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 20.77 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.008 0.001 PHE E 42 TYR 0.013 0.002 TYR G 21 ARG 0.005 0.002 ARG L 54 *********************** 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 279 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.779 Fit side-chains REVERT: B 41 TYR cc_start: 0.8726 (m-80) cc_final: 0.8467 (m-80) REVERT: C 33 GLU cc_start: 0.7904 (tt0) cc_final: 0.7559 (tm-30) REVERT: E 24 ASP cc_start: 0.8288 (m-30) cc_final: 0.7975 (m-30) REVERT: G 71 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7414 (mt-10) REVERT: M 68 MET cc_start: 0.8767 (ttp) cc_final: 0.8527 (ttm) outliers start: 17 outliers final: 4 residues processed: 269 average time/residue: 1.1916 time to fit residues: 335.9809 Evaluate side-chains 247 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain I residue 12 THR 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 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 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 13 GLN ** 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** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107393 restraints weight = 7549.136| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.43 r_work: 0.3523 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6636 Z= 0.320 Angle : 0.719 7.122 8904 Z= 0.361 Chirality : 0.045 0.141 984 Planarity : 0.005 0.056 1140 Dihedral : 6.378 22.449 852 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 22.81 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 46 PHE 0.010 0.002 PHE N 42 TYR 0.013 0.002 TYR E 21 ARG 0.005 0.002 ARG I 54 *********************** 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 272 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.810 Fit side-chains REVERT: B 28 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8641 (mppt) REVERT: B 41 TYR cc_start: 0.8687 (m-80) cc_final: 0.8484 (m-80) REVERT: C 33 GLU cc_start: 0.7996 (tt0) cc_final: 0.7663 (tm-30) REVERT: E 24 ASP cc_start: 0.8599 (m-30) cc_final: 0.8306 (m-30) REVERT: H 9 SER cc_start: 0.8860 (p) cc_final: 0.8632 (m) REVERT: L 50 THR cc_start: 0.8907 (m) cc_final: 0.8553 (p) outliers start: 20 outliers final: 9 residues processed: 262 average time/residue: 1.2411 time to fit residues: 339.8589 Evaluate side-chains 251 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain I residue 12 THR 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 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** 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** ** 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 = 0.3786 r_free = 0.3786 target = 0.117593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108619 restraints weight = 7498.596| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.38 r_work: 0.3544 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5862 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= 0.283 Angle : 0.694 7.326 8904 Z= 0.347 Chirality : 0.044 0.129 984 Planarity : 0.005 0.049 1140 Dihedral : 6.168 22.013 852 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.73 % Allowed : 24.32 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.008 0.001 PHE N 42 TYR 0.012 0.002 TYR H 41 ARG 0.004 0.001 ARG H 54 *********************** 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 274 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.732 Fit side-chains REVERT: B 28 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8443 (mppt) REVERT: C 33 GLU cc_start: 0.7955 (tt0) cc_final: 0.7630 (tm-30) REVERT: E 24 ASP cc_start: 0.8580 (m-30) cc_final: 0.8282 (m-30) REVERT: H 9 SER cc_start: 0.8874 (p) cc_final: 0.8648 (m) REVERT: N 41 TYR cc_start: 0.8436 (m-80) cc_final: 0.8168 (m-80) outliers start: 20 outliers final: 10 residues processed: 263 average time/residue: 1.2370 time to fit residues: 340.2311 Evaluate side-chains 259 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain E residue 52 LEU 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 52 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 24 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107941 restraints weight = 7449.154| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.38 r_work: 0.3540 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6636 Z= 0.289 Angle : 0.698 6.912 8904 Z= 0.350 Chirality : 0.044 0.131 984 Planarity : 0.005 0.051 1140 Dihedral : 6.125 21.452 852 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.60 % Allowed : 26.64 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE B 11 TYR 0.014 0.002 TYR H 41 ARG 0.004 0.001 ARG I 54 *********************** 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 266 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.123 Fit side-chains REVERT: B 28 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8497 (mppt) REVERT: C 33 GLU cc_start: 0.7954 (tt0) cc_final: 0.7616 (tm-30) REVERT: E 24 ASP cc_start: 0.8633 (m-30) cc_final: 0.8360 (m-30) REVERT: G 24 ASP cc_start: 0.8890 (m-30) cc_final: 0.8677 (m-30) REVERT: H 9 SER cc_start: 0.8887 (p) cc_final: 0.8653 (m) REVERT: N 41 TYR cc_start: 0.8408 (m-80) cc_final: 0.8106 (m-80) outliers start: 19 outliers final: 11 residues processed: 257 average time/residue: 1.2819 time to fit residues: 344.6670 Evaluate side-chains 256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR 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 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 32 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3767 r_free = 0.3767 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106908 restraints weight = 7432.054| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.39 r_work: 0.3519 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.6059 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= 0.325 Angle : 0.719 7.330 8904 Z= 0.363 Chirality : 0.045 0.134 984 Planarity : 0.005 0.057 1140 Dihedral : 6.223 21.853 852 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.46 % Allowed : 26.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.008 0.001 PHE B 11 TYR 0.013 0.002 TYR H 41 ARG 0.004 0.001 ARG I 54 *********************** 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 266 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.837 Fit side-chains REVERT: A 43 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: B 28 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8521 (mppt) REVERT: C 33 GLU cc_start: 0.7976 (tt0) cc_final: 0.7653 (tm-30) REVERT: E 24 ASP cc_start: 0.8664 (m-30) cc_final: 0.8395 (m-30) REVERT: I 71 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7404 (mt-10) REVERT: N 41 TYR cc_start: 0.8446 (m-80) cc_final: 0.8129 (m-80) outliers start: 18 outliers final: 10 residues processed: 259 average time/residue: 1.2775 time to fit residues: 345.6878 Evaluate side-chains 256 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 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 27 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.106222 restraints weight = 7490.999| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.42 r_work: 0.3505 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6636 Z= 0.342 Angle : 0.734 7.695 8904 Z= 0.370 Chirality : 0.045 0.135 984 Planarity : 0.005 0.059 1140 Dihedral : 6.281 22.048 852 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.05 % Allowed : 27.19 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.21), 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 HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE E 11 TYR 0.014 0.002 TYR M 41 ARG 0.003 0.001 ARG M 54 *********************** 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 257 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.842 Fit side-chains REVERT: A 43 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 28 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8651 (mppt) REVERT: C 33 GLU cc_start: 0.7972 (tt0) cc_final: 0.7644 (tm-30) REVERT: E 24 ASP cc_start: 0.8662 (m-30) cc_final: 0.8352 (m-30) REVERT: I 71 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7516 (mt-10) REVERT: N 41 TYR cc_start: 0.8485 (m-80) cc_final: 0.8236 (m-80) outliers start: 15 outliers final: 8 residues processed: 251 average time/residue: 1.3328 time to fit residues: 349.0671 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 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 58 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106120 restraints weight = 7555.972| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.41 r_work: 0.3515 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.6129 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= 0.314 Angle : 0.717 7.100 8904 Z= 0.363 Chirality : 0.045 0.133 984 Planarity : 0.005 0.055 1140 Dihedral : 6.197 21.679 852 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.64 % Allowed : 28.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS D 46 PHE 0.008 0.001 PHE E 11 TYR 0.014 0.002 TYR H 41 ARG 0.004 0.001 ARG I 54 *********************** 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 252 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.834 Fit side-chains REVERT: A 43 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: B 28 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (mppt) REVERT: C 33 GLU cc_start: 0.7958 (tt0) cc_final: 0.7630 (tm-30) REVERT: E 24 ASP cc_start: 0.8649 (m-30) cc_final: 0.8343 (m-30) REVERT: I 71 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7617 (mt-10) REVERT: N 41 TYR cc_start: 0.8478 (m-80) cc_final: 0.8221 (m-80) outliers start: 12 outliers final: 9 residues processed: 245 average time/residue: 1.2759 time to fit residues: 326.4785 Evaluate side-chains 248 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 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 12 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.107638 restraints weight = 7517.454| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.39 r_work: 0.3534 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.6144 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= 0.275 Angle : 0.711 6.857 8904 Z= 0.357 Chirality : 0.044 0.131 984 Planarity : 0.005 0.050 1140 Dihedral : 6.036 20.921 852 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE B 11 TYR 0.014 0.002 TYR M 41 ARG 0.004 0.001 ARG I 54 ********************** 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 258 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.844 Fit side-chains REVERT: A 43 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 33 GLU cc_start: 0.7961 (tt0) cc_final: 0.7634 (tm-30) REVERT: E 24 ASP cc_start: 0.8617 (m-30) cc_final: 0.8291 (m-30) REVERT: N 41 TYR cc_start: 0.8462 (m-80) cc_final: 0.8179 (m-80) outliers start: 14 outliers final: 12 residues processed: 249 average time/residue: 1.2706 time to fit residues: 330.4425 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 : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR 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 N residue 28 LYS Chi-restraints excluded: chain N residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.106850 restraints weight = 7656.969| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.43 r_work: 0.3519 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6636 Z= 0.293 Angle : 0.714 7.008 8904 Z= 0.360 Chirality : 0.045 0.134 984 Planarity : 0.005 0.052 1140 Dihedral : 6.093 20.812 852 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.91 % Allowed : 28.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE B 11 TYR 0.014 0.002 TYR M 41 ARG 0.003 0.001 ARG I 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7072.56 seconds wall clock time: 120 minutes 49.87 seconds (7249.87 seconds total)