Starting phenix.real_space_refine on Wed Jul 23 10:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1k_41815/07_2025/8u1k_41815.cif" } resolution = 3.5 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= -0.001 sd= 0.017 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: 3 Type Number sf(0) Gaussians C 1970 2.51 5 N 500 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.82, per 1000 atoms: 0.59 Number of scatterers: 3060 At special positions: 0 Unit cell: (58.38, 57.546, 118.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 590 8.00 N 500 7.00 C 1970 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: 0.78 Conformation dependent library (CDL) restraints added in 390.6 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 5 No H-bonds generated for 'chain 'E' and resid 3 through 5' Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 5 No H-bonds generated for 'chain 'F' and resid 3 through 5' Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR G 30 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR H 30 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR I 30 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 6 through 11 Processing helix chain 'J' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 630 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: 0.73 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 480 1.29 - 1.35: 480 1.35 - 1.42: 140 1.42 - 1.48: 550 1.48 - 1.54: 1420 Bond restraints: 3070 Sorted by residual: bond pdb=" CA ALA E 38 " pdb=" C ALA E 38 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.29e-02 6.01e+03 4.38e-01 bond pdb=" CA ALA A 38 " pdb=" C ALA A 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 4.00e-01 bond pdb=" CA ALA C 38 " pdb=" C ALA C 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.96e-01 bond pdb=" CA ALA I 38 " pdb=" C ALA I 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.85e-01 bond pdb=" N ALA F 38 " pdb=" CA ALA F 38 " ideal model delta sigma weight residual 1.459 1.451 0.008 1.24e-02 6.50e+03 3.84e-01 ... (remaining 3065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.65: 3507 0.65 - 1.30: 468 1.30 - 1.95: 195 1.95 - 2.60: 30 2.60 - 3.25: 20 Bond angle restraints: 4220 Sorted by residual: angle pdb=" N ILE G 4 " pdb=" CA ILE G 4 " pdb=" C ILE G 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.44e+00 angle pdb=" N ILE F 4 " pdb=" CA ILE F 4 " pdb=" C ILE F 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" C ILE A 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.42e+00 angle pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" C ILE B 4 " ideal model delta sigma weight residual 109.34 112.56 -3.22 2.08e+00 2.31e-01 2.40e+00 ... (remaining 4215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.83: 1500 9.83 - 19.66: 140 19.66 - 29.49: 70 29.49 - 39.32: 30 39.32 - 49.16: 30 Dihedral angle restraints: 1770 sinusoidal: 500 harmonic: 1270 Sorted by residual: dihedral pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" CB ILE A 4 " pdb=" CG1 ILE A 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.84 -49.16 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" CB ILE B 4 " pdb=" CG1 ILE B 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.85 -49.15 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE I 4 " pdb=" CA ILE I 4 " pdb=" CB ILE I 4 " pdb=" CG1 ILE I 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.90 -49.10 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 282 0.021 - 0.041: 173 0.041 - 0.062: 95 0.062 - 0.083: 50 0.083 - 0.103: 40 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA THR F 30 " pdb=" N THR F 30 " pdb=" C THR F 30 " pdb=" CB THR F 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA THR A 30 " pdb=" N THR A 30 " pdb=" C THR A 30 " pdb=" CB THR A 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA THR J 30 " pdb=" N THR J 30 " pdb=" C THR J 30 " pdb=" CB THR J 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.57e-01 ... (remaining 637 not shown) Planarity restraints: 490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 25 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLY F 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY F 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR F 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 25 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY J 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY J 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR J 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 25 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY G 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY G 25 " -0.010 2.00e-02 2.50e+03 pdb=" N THR G 26 " -0.009 2.00e-02 2.50e+03 ... (remaining 487 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 509 2.74 - 3.28: 3380 3.28 - 3.82: 5155 3.82 - 4.36: 5996 4.36 - 4.90: 9519 Nonbonded interactions: 24559 Sorted by model distance: nonbonded pdb=" O ARG D 29 " pdb=" OG1 THR D 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG A 29 " pdb=" OG1 THR A 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG J 29 " pdb=" OG1 THR J 33 " model vdw 2.206 3.040 nonbonded pdb=" O ARG H 29 " pdb=" OG1 THR H 33 " model vdw 2.207 3.040 nonbonded pdb=" O ARG B 29 " pdb=" OG1 THR B 33 " model vdw 2.207 3.040 ... (remaining 24554 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: 0.03 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 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3070 Z= 0.203 Angle : 0.609 3.251 4220 Z= 0.377 Chirality : 0.040 0.103 640 Planarity : 0.003 0.015 490 Dihedral : 13.638 49.155 950 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.99 (0.23), residues: 430 helix: -3.55 (0.17), residues: 340 sheet: None (None), residues: 0 loop : -4.60 (0.29), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE B 32 TYR 0.003 0.001 TYR C 6 ARG 0.002 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 210) hydrogen bonds : angle 4.99398 ( 630) covalent geometry : bond 0.00371 ( 3070) covalent geometry : angle 0.60898 ( 4220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8181 (m) cc_final: 0.7831 (p) REVERT: A 23 THR cc_start: 0.7918 (m) cc_final: 0.7493 (p) REVERT: A 24 LEU cc_start: 0.8794 (tp) cc_final: 0.8574 (tp) REVERT: A 26 THR cc_start: 0.7855 (t) cc_final: 0.7535 (m) REVERT: A 29 ARG cc_start: 0.6708 (mtt180) cc_final: 0.6429 (mtt-85) REVERT: B 18 VAL cc_start: 0.8584 (t) cc_final: 0.8291 (m) REVERT: B 23 THR cc_start: 0.7839 (m) cc_final: 0.7286 (p) REVERT: B 24 LEU cc_start: 0.8771 (tp) cc_final: 0.8388 (tp) REVERT: B 34 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7291 (mtmm) REVERT: C 18 VAL cc_start: 0.8548 (t) cc_final: 0.8287 (m) REVERT: C 23 THR cc_start: 0.7859 (m) cc_final: 0.7351 (p) REVERT: D 4 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (mp) REVERT: D 18 VAL cc_start: 0.8513 (t) cc_final: 0.8287 (m) REVERT: D 23 THR cc_start: 0.7891 (m) cc_final: 0.7252 (p) REVERT: D 24 LEU cc_start: 0.8740 (tp) cc_final: 0.8516 (tp) REVERT: D 27 ASN cc_start: 0.7039 (m-40) cc_final: 0.6792 (m110) REVERT: E 18 VAL cc_start: 0.8614 (t) cc_final: 0.8289 (m) REVERT: E 27 ASN cc_start: 0.7090 (m-40) cc_final: 0.6838 (m110) REVERT: F 23 THR cc_start: 0.7904 (m) cc_final: 0.7425 (p) REVERT: F 26 THR cc_start: 0.8031 (t) cc_final: 0.7751 (m) REVERT: F 29 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6464 (mtt-85) REVERT: G 23 THR cc_start: 0.7990 (m) cc_final: 0.7534 (p) REVERT: G 24 LEU cc_start: 0.8864 (tp) cc_final: 0.8451 (tt) REVERT: G 26 THR cc_start: 0.8044 (t) cc_final: 0.7399 (m) REVERT: G 29 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6245 (mtt-85) REVERT: H 23 THR cc_start: 0.8003 (m) cc_final: 0.7600 (p) REVERT: H 24 LEU cc_start: 0.8858 (tp) cc_final: 0.8618 (tp) REVERT: I 23 THR cc_start: 0.7899 (m) cc_final: 0.7374 (p) REVERT: I 24 LEU cc_start: 0.8800 (tp) cc_final: 0.8525 (tp) REVERT: J 18 VAL cc_start: 0.8554 (t) cc_final: 0.8304 (m) REVERT: J 23 THR cc_start: 0.7933 (m) cc_final: 0.7479 (p) REVERT: J 24 LEU cc_start: 0.8856 (tp) cc_final: 0.8403 (tt) REVERT: J 34 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7102 (mtmm) outliers start: 10 outliers final: 6 residues processed: 224 average time/residue: 0.1276 time to fit residues: 34.1128 Evaluate side-chains 222 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 4 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089878 restraints weight = 5751.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092118 restraints weight = 2700.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093534 restraints weight = 1573.047| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3070 Z= 0.127 Angle : 0.507 4.625 4220 Z= 0.286 Chirality : 0.038 0.099 640 Planarity : 0.003 0.033 490 Dihedral : 8.630 55.240 474 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 10.00 % Allowed : 32.00 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.33 (0.32), residues: 430 helix: -2.43 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.74 (0.41), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE I 32 TYR 0.007 0.002 TYR H 6 ARG 0.008 0.001 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 210) hydrogen bonds : angle 4.45657 ( 630) covalent geometry : bond 0.00241 ( 3070) covalent geometry : angle 0.50661 ( 4220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8076 (m) cc_final: 0.7823 (p) REVERT: A 18 VAL cc_start: 0.8775 (t) cc_final: 0.8521 (m) REVERT: A 23 THR cc_start: 0.7848 (m) cc_final: 0.7381 (p) REVERT: B 23 THR cc_start: 0.7832 (m) cc_final: 0.7313 (p) REVERT: C 4 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7911 (mp) REVERT: C 23 THR cc_start: 0.7740 (m) cc_final: 0.7278 (p) REVERT: C 28 LEU cc_start: 0.8718 (tp) cc_final: 0.8454 (tt) REVERT: D 18 VAL cc_start: 0.8592 (t) cc_final: 0.8314 (m) REVERT: D 23 THR cc_start: 0.7860 (m) cc_final: 0.7240 (p) REVERT: D 27 ASN cc_start: 0.6822 (m-40) cc_final: 0.6538 (m110) REVERT: E 18 VAL cc_start: 0.8674 (t) cc_final: 0.8348 (m) REVERT: F 23 THR cc_start: 0.7848 (m) cc_final: 0.7366 (p) REVERT: F 26 THR cc_start: 0.8017 (t) cc_final: 0.7663 (m) REVERT: G 23 THR cc_start: 0.7957 (m) cc_final: 0.7484 (p) REVERT: G 24 LEU cc_start: 0.8690 (tp) cc_final: 0.8378 (tt) REVERT: G 26 THR cc_start: 0.8119 (t) cc_final: 0.7680 (t) REVERT: H 23 THR cc_start: 0.7911 (m) cc_final: 0.7498 (p) REVERT: H 24 LEU cc_start: 0.8825 (tp) cc_final: 0.8583 (tp) REVERT: I 23 THR cc_start: 0.7692 (m) cc_final: 0.7234 (p) REVERT: I 24 LEU cc_start: 0.8735 (tp) cc_final: 0.8501 (tp) REVERT: J 18 VAL cc_start: 0.8634 (t) cc_final: 0.8407 (m) REVERT: J 23 THR cc_start: 0.7721 (m) cc_final: 0.7343 (p) REVERT: J 24 LEU cc_start: 0.8771 (tp) cc_final: 0.8333 (tt) outliers start: 30 outliers final: 24 residues processed: 219 average time/residue: 0.1315 time to fit residues: 34.5985 Evaluate side-chains 237 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 17 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091870 restraints weight = 5766.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094104 restraints weight = 2705.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095521 restraints weight = 1560.771| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3070 Z= 0.130 Angle : 0.541 6.506 4220 Z= 0.299 Chirality : 0.039 0.118 640 Planarity : 0.004 0.047 490 Dihedral : 6.713 47.108 470 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 12.00 % Allowed : 32.67 % Favored : 55.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.13 (0.32), residues: 430 helix: -2.29 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.68 (0.36), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE H 32 TYR 0.010 0.001 TYR D 6 ARG 0.009 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 210) hydrogen bonds : angle 4.20655 ( 630) covalent geometry : bond 0.00248 ( 3070) covalent geometry : angle 0.54110 ( 4220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8050 (m) cc_final: 0.7770 (p) REVERT: A 23 THR cc_start: 0.7868 (m) cc_final: 0.7434 (p) REVERT: B 18 VAL cc_start: 0.8735 (t) cc_final: 0.8527 (m) REVERT: B 23 THR cc_start: 0.7850 (m) cc_final: 0.7433 (p) REVERT: C 23 THR cc_start: 0.7762 (m) cc_final: 0.7283 (p) REVERT: D 18 VAL cc_start: 0.8569 (t) cc_final: 0.8264 (m) REVERT: D 23 THR cc_start: 0.7911 (m) cc_final: 0.7293 (p) REVERT: D 24 LEU cc_start: 0.8438 (tp) cc_final: 0.7539 (mm) REVERT: D 27 ASN cc_start: 0.6722 (m-40) cc_final: 0.6352 (m110) REVERT: E 18 VAL cc_start: 0.8553 (t) cc_final: 0.8279 (m) REVERT: F 23 THR cc_start: 0.7736 (m) cc_final: 0.7152 (p) REVERT: G 22 THR cc_start: 0.8554 (m) cc_final: 0.8343 (p) REVERT: G 23 THR cc_start: 0.7911 (m) cc_final: 0.7278 (p) REVERT: G 24 LEU cc_start: 0.8485 (tp) cc_final: 0.8197 (tt) REVERT: H 23 THR cc_start: 0.7890 (m) cc_final: 0.7532 (p) REVERT: H 24 LEU cc_start: 0.8801 (tp) cc_final: 0.8584 (tp) REVERT: I 23 THR cc_start: 0.7727 (m) cc_final: 0.7316 (p) REVERT: I 24 LEU cc_start: 0.8746 (tp) cc_final: 0.8365 (tt) REVERT: I 39 VAL cc_start: 0.8487 (p) cc_final: 0.8281 (t) REVERT: J 23 THR cc_start: 0.7741 (m) cc_final: 0.7460 (p) REVERT: J 24 LEU cc_start: 0.8797 (tp) cc_final: 0.8370 (tt) REVERT: J 34 LYS cc_start: 0.7404 (mtmt) cc_final: 0.7101 (mtmm) outliers start: 36 outliers final: 28 residues processed: 222 average time/residue: 0.1321 time to fit residues: 35.2703 Evaluate side-chains 242 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 ASN J 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.101784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092001 restraints weight = 5924.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094160 restraints weight = 2764.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095585 restraints weight = 1609.626| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3070 Z= 0.139 Angle : 0.536 5.780 4220 Z= 0.299 Chirality : 0.040 0.145 640 Planarity : 0.005 0.055 490 Dihedral : 6.117 51.019 468 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 14.67 % Allowed : 34.00 % Favored : 51.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.98 (0.32), residues: 430 helix: -2.20 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.55 (0.36), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 32 TYR 0.006 0.001 TYR D 6 ARG 0.008 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 210) hydrogen bonds : angle 4.19976 ( 630) covalent geometry : bond 0.00271 ( 3070) covalent geometry : angle 0.53626 ( 4220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8038 (m) cc_final: 0.7769 (p) REVERT: A 23 THR cc_start: 0.7841 (m) cc_final: 0.7424 (p) REVERT: B 23 THR cc_start: 0.7977 (m) cc_final: 0.7564 (p) REVERT: C 5 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 18 VAL cc_start: 0.8591 (p) cc_final: 0.8313 (t) REVERT: C 23 THR cc_start: 0.7756 (m) cc_final: 0.7285 (p) REVERT: D 18 VAL cc_start: 0.8583 (t) cc_final: 0.8247 (m) REVERT: D 23 THR cc_start: 0.7839 (m) cc_final: 0.7202 (p) REVERT: D 24 LEU cc_start: 0.8294 (tp) cc_final: 0.7260 (mm) REVERT: E 18 VAL cc_start: 0.8459 (t) cc_final: 0.8171 (m) REVERT: E 27 ASN cc_start: 0.7157 (m-40) cc_final: 0.6918 (m110) REVERT: F 23 THR cc_start: 0.7848 (m) cc_final: 0.7386 (p) REVERT: F 24 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8286 (tt) REVERT: G 23 THR cc_start: 0.7923 (m) cc_final: 0.7414 (p) REVERT: G 24 LEU cc_start: 0.8523 (tp) cc_final: 0.8292 (tt) REVERT: H 23 THR cc_start: 0.7895 (m) cc_final: 0.7549 (p) REVERT: H 24 LEU cc_start: 0.8780 (tp) cc_final: 0.8575 (tp) REVERT: I 23 THR cc_start: 0.7742 (m) cc_final: 0.7301 (p) REVERT: I 24 LEU cc_start: 0.8721 (tp) cc_final: 0.8335 (tt) REVERT: J 2 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7308 (p) REVERT: J 23 THR cc_start: 0.7721 (m) cc_final: 0.7401 (p) REVERT: J 24 LEU cc_start: 0.8835 (tp) cc_final: 0.8438 (tt) outliers start: 44 outliers final: 37 residues processed: 222 average time/residue: 0.1299 time to fit residues: 34.6442 Evaluate side-chains 250 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091123 restraints weight = 5810.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093370 restraints weight = 2806.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094737 restraints weight = 1663.283| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3070 Z= 0.208 Angle : 0.573 5.097 4220 Z= 0.327 Chirality : 0.042 0.130 640 Planarity : 0.005 0.057 490 Dihedral : 5.691 41.755 466 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 14.67 % Allowed : 35.67 % Favored : 49.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.29 (0.31), residues: 430 helix: -2.45 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.51 (0.35), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 32 TYR 0.005 0.001 TYR D 6 ARG 0.008 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 210) hydrogen bonds : angle 4.58158 ( 630) covalent geometry : bond 0.00378 ( 3070) covalent geometry : angle 0.57327 ( 4220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8135 (m) cc_final: 0.7852 (p) REVERT: A 22 THR cc_start: 0.8471 (m) cc_final: 0.8266 (p) REVERT: A 23 THR cc_start: 0.7801 (m) cc_final: 0.7300 (p) REVERT: B 23 THR cc_start: 0.8013 (m) cc_final: 0.7633 (p) REVERT: C 23 THR cc_start: 0.7843 (m) cc_final: 0.7306 (p) REVERT: D 18 VAL cc_start: 0.8522 (t) cc_final: 0.8197 (m) REVERT: D 23 THR cc_start: 0.7898 (m) cc_final: 0.7235 (p) REVERT: D 27 ASN cc_start: 0.7176 (m-40) cc_final: 0.6939 (m110) REVERT: E 18 VAL cc_start: 0.8484 (t) cc_final: 0.8187 (m) REVERT: E 27 ASN cc_start: 0.7216 (m-40) cc_final: 0.6807 (m110) REVERT: F 23 THR cc_start: 0.8080 (m) cc_final: 0.7532 (p) REVERT: F 24 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8382 (tt) REVERT: F 27 ASN cc_start: 0.6551 (m-40) cc_final: 0.6112 (m-40) REVERT: F 28 LEU cc_start: 0.8641 (tp) cc_final: 0.8414 (tt) REVERT: G 23 THR cc_start: 0.8029 (m) cc_final: 0.7526 (p) REVERT: G 24 LEU cc_start: 0.8643 (tp) cc_final: 0.8376 (tt) REVERT: H 23 THR cc_start: 0.7928 (m) cc_final: 0.7588 (p) REVERT: H 24 LEU cc_start: 0.8852 (tp) cc_final: 0.8602 (tp) REVERT: I 23 THR cc_start: 0.7761 (m) cc_final: 0.7285 (p) REVERT: I 24 LEU cc_start: 0.8764 (tp) cc_final: 0.8336 (tt) REVERT: J 2 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7449 (p) REVERT: J 23 THR cc_start: 0.7727 (m) cc_final: 0.7212 (p) REVERT: J 24 LEU cc_start: 0.8782 (tp) cc_final: 0.8424 (tt) REVERT: J 27 ASN cc_start: 0.7124 (m110) cc_final: 0.6706 (m110) REVERT: J 34 LYS cc_start: 0.7363 (mtmt) cc_final: 0.7068 (mtmm) outliers start: 44 outliers final: 37 residues processed: 223 average time/residue: 0.1304 time to fit residues: 34.8583 Evaluate side-chains 250 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095198 restraints weight = 5992.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097438 restraints weight = 2825.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098820 restraints weight = 1619.574| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3070 Z= 0.123 Angle : 0.573 5.885 4220 Z= 0.312 Chirality : 0.039 0.108 640 Planarity : 0.004 0.041 490 Dihedral : 4.777 35.754 464 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 13.00 % Allowed : 36.33 % Favored : 50.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.44 (0.34), residues: 430 helix: -1.82 (0.26), residues: 340 sheet: None (None), residues: 0 loop : -3.35 (0.37), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 32 TYR 0.005 0.001 TYR G 6 ARG 0.009 0.002 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 210) hydrogen bonds : angle 4.02996 ( 630) covalent geometry : bond 0.00255 ( 3070) covalent geometry : angle 0.57320 ( 4220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8193 (mt) cc_final: 0.7878 (mt) REVERT: A 16 VAL cc_start: 0.8010 (m) cc_final: 0.7751 (p) REVERT: A 18 VAL cc_start: 0.8804 (t) cc_final: 0.8524 (m) REVERT: A 23 THR cc_start: 0.7633 (m) cc_final: 0.7254 (p) REVERT: B 23 THR cc_start: 0.7863 (m) cc_final: 0.7501 (p) REVERT: C 23 THR cc_start: 0.7690 (m) cc_final: 0.7203 (p) REVERT: C 24 LEU cc_start: 0.8398 (tp) cc_final: 0.7388 (mm) REVERT: D 18 VAL cc_start: 0.8502 (t) cc_final: 0.8247 (m) REVERT: D 23 THR cc_start: 0.7740 (m) cc_final: 0.7026 (p) REVERT: D 24 LEU cc_start: 0.8190 (tp) cc_final: 0.7175 (mm) REVERT: D 27 ASN cc_start: 0.6995 (m-40) cc_final: 0.6778 (m110) REVERT: D 34 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7292 (mtmm) REVERT: E 26 THR cc_start: 0.7960 (m) cc_final: 0.7629 (m) REVERT: E 27 ASN cc_start: 0.7086 (m-40) cc_final: 0.6855 (m110) REVERT: F 23 THR cc_start: 0.7852 (m) cc_final: 0.7382 (p) REVERT: F 24 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8096 (tt) REVERT: F 27 ASN cc_start: 0.6482 (m-40) cc_final: 0.6118 (m-40) REVERT: G 23 THR cc_start: 0.7990 (m) cc_final: 0.7495 (p) REVERT: G 24 LEU cc_start: 0.8481 (tp) cc_final: 0.8258 (tt) REVERT: H 23 THR cc_start: 0.7848 (m) cc_final: 0.7524 (p) REVERT: H 24 LEU cc_start: 0.8761 (tp) cc_final: 0.8556 (tp) REVERT: I 16 VAL cc_start: 0.8053 (p) cc_final: 0.7405 (m) REVERT: I 23 THR cc_start: 0.7707 (m) cc_final: 0.7263 (p) REVERT: I 24 LEU cc_start: 0.8718 (tp) cc_final: 0.8293 (tt) REVERT: J 2 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7427 (p) REVERT: J 23 THR cc_start: 0.7732 (m) cc_final: 0.7433 (p) REVERT: J 24 LEU cc_start: 0.8810 (tp) cc_final: 0.8421 (tt) outliers start: 39 outliers final: 32 residues processed: 216 average time/residue: 0.1318 time to fit residues: 33.9583 Evaluate side-chains 236 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093618 restraints weight = 5844.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095771 restraints weight = 2791.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097173 restraints weight = 1658.106| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3070 Z= 0.172 Angle : 0.638 7.570 4220 Z= 0.350 Chirality : 0.042 0.200 640 Planarity : 0.004 0.032 490 Dihedral : 4.922 33.773 464 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 13.00 % Allowed : 38.00 % Favored : 49.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.33), residues: 430 helix: -2.06 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.29 (0.40), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 32 TYR 0.012 0.001 TYR C 6 ARG 0.006 0.001 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 210) hydrogen bonds : angle 4.41639 ( 630) covalent geometry : bond 0.00338 ( 3070) covalent geometry : angle 0.63808 ( 4220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8081 (m) cc_final: 0.7804 (p) REVERT: A 23 THR cc_start: 0.7794 (m) cc_final: 0.7437 (p) REVERT: B 23 THR cc_start: 0.7908 (m) cc_final: 0.7528 (p) REVERT: C 23 THR cc_start: 0.7763 (m) cc_final: 0.7070 (p) REVERT: C 24 LEU cc_start: 0.8440 (tp) cc_final: 0.7427 (mm) REVERT: C 27 ASN cc_start: 0.6638 (m-40) cc_final: 0.6280 (m110) REVERT: D 18 VAL cc_start: 0.8499 (t) cc_final: 0.8065 (m) REVERT: D 23 THR cc_start: 0.7767 (m) cc_final: 0.7134 (p) REVERT: D 34 LYS cc_start: 0.7444 (mtmm) cc_final: 0.7164 (mtmm) REVERT: E 18 VAL cc_start: 0.8353 (t) cc_final: 0.8109 (m) REVERT: F 23 THR cc_start: 0.8034 (m) cc_final: 0.7322 (p) REVERT: F 24 LEU cc_start: 0.8522 (tp) cc_final: 0.8291 (tt) REVERT: F 27 ASN cc_start: 0.6347 (m-40) cc_final: 0.5754 (m-40) REVERT: F 30 THR cc_start: 0.7658 (t) cc_final: 0.7385 (m) REVERT: G 23 THR cc_start: 0.8035 (m) cc_final: 0.7546 (p) REVERT: G 24 LEU cc_start: 0.8597 (tp) cc_final: 0.8373 (tt) REVERT: H 16 VAL cc_start: 0.7746 (m) cc_final: 0.6569 (p) REVERT: H 23 THR cc_start: 0.7887 (m) cc_final: 0.7531 (p) REVERT: I 16 VAL cc_start: 0.7872 (p) cc_final: 0.7170 (t) REVERT: I 23 THR cc_start: 0.7753 (m) cc_final: 0.7297 (p) REVERT: I 24 LEU cc_start: 0.8726 (tp) cc_final: 0.8312 (tt) REVERT: J 23 THR cc_start: 0.7676 (m) cc_final: 0.7382 (p) REVERT: J 24 LEU cc_start: 0.8818 (tp) cc_final: 0.8419 (tt) REVERT: J 34 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7080 (mtmm) outliers start: 39 outliers final: 35 residues processed: 219 average time/residue: 0.1329 time to fit residues: 34.9866 Evaluate side-chains 241 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN E 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092603 restraints weight = 5782.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094856 restraints weight = 2792.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.096286 restraints weight = 1663.935| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3070 Z= 0.195 Angle : 0.668 7.566 4220 Z= 0.359 Chirality : 0.046 0.214 640 Planarity : 0.005 0.073 490 Dihedral : 4.685 19.525 460 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 14.33 % Allowed : 38.67 % Favored : 47.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.95 (0.32), residues: 430 helix: -2.23 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.28 (0.39), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE D 32 TYR 0.008 0.001 TYR G 6 ARG 0.010 0.002 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 210) hydrogen bonds : angle 4.59225 ( 630) covalent geometry : bond 0.00382 ( 3070) covalent geometry : angle 0.66807 ( 4220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8083 (m) cc_final: 0.7818 (p) REVERT: A 18 VAL cc_start: 0.8966 (t) cc_final: 0.8708 (m) REVERT: A 23 THR cc_start: 0.8142 (m) cc_final: 0.7609 (p) REVERT: A 34 LYS cc_start: 0.7425 (mtmm) cc_final: 0.7007 (mtmt) REVERT: B 23 THR cc_start: 0.7934 (m) cc_final: 0.7555 (p) REVERT: C 23 THR cc_start: 0.7935 (m) cc_final: 0.7052 (p) REVERT: C 24 LEU cc_start: 0.8539 (tp) cc_final: 0.7489 (mm) REVERT: C 27 ASN cc_start: 0.6685 (m-40) cc_final: 0.6121 (m110) REVERT: D 18 VAL cc_start: 0.8661 (t) cc_final: 0.8341 (m) REVERT: D 23 THR cc_start: 0.7841 (m) cc_final: 0.7344 (p) REVERT: D 24 LEU cc_start: 0.8565 (tp) cc_final: 0.8272 (tt) REVERT: E 18 VAL cc_start: 0.8450 (t) cc_final: 0.8148 (m) REVERT: E 27 ASN cc_start: 0.6754 (m-40) cc_final: 0.6445 (m110) REVERT: F 23 THR cc_start: 0.7973 (m) cc_final: 0.7207 (p) REVERT: F 24 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8249 (tt) REVERT: F 27 ASN cc_start: 0.6342 (m-40) cc_final: 0.5663 (m-40) REVERT: F 30 THR cc_start: 0.7559 (t) cc_final: 0.7344 (m) REVERT: G 23 THR cc_start: 0.8081 (m) cc_final: 0.7590 (p) REVERT: G 24 LEU cc_start: 0.8641 (tp) cc_final: 0.8387 (tt) REVERT: H 23 THR cc_start: 0.7857 (m) cc_final: 0.7519 (p) REVERT: I 23 THR cc_start: 0.7815 (m) cc_final: 0.7318 (p) REVERT: I 24 LEU cc_start: 0.8730 (tp) cc_final: 0.8279 (tt) REVERT: J 23 THR cc_start: 0.7710 (m) cc_final: 0.7431 (p) REVERT: J 24 LEU cc_start: 0.8804 (tp) cc_final: 0.8352 (tt) outliers start: 43 outliers final: 37 residues processed: 213 average time/residue: 0.1359 time to fit residues: 35.0276 Evaluate side-chains 240 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094208 restraints weight = 5857.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096464 restraints weight = 2818.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097840 restraints weight = 1665.701| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3070 Z= 0.142 Angle : 0.665 8.663 4220 Z= 0.341 Chirality : 0.043 0.204 640 Planarity : 0.004 0.053 490 Dihedral : 4.510 17.128 460 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 12.33 % Allowed : 41.00 % Favored : 46.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.48 (0.34), residues: 430 helix: -1.92 (0.25), residues: 340 sheet: None (None), residues: 0 loop : -3.01 (0.42), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE E 32 TYR 0.008 0.001 TYR G 6 ARG 0.008 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 210) hydrogen bonds : angle 4.20914 ( 630) covalent geometry : bond 0.00308 ( 3070) covalent geometry : angle 0.66481 ( 4220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.7999 (m) cc_final: 0.7748 (p) REVERT: A 18 VAL cc_start: 0.8966 (t) cc_final: 0.8708 (m) REVERT: A 23 THR cc_start: 0.8095 (m) cc_final: 0.7590 (p) REVERT: A 34 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6926 (mtmt) REVERT: B 23 THR cc_start: 0.7866 (m) cc_final: 0.7500 (p) REVERT: C 23 THR cc_start: 0.7918 (m) cc_final: 0.7395 (p) REVERT: C 24 LEU cc_start: 0.8408 (tp) cc_final: 0.7397 (mm) REVERT: D 18 VAL cc_start: 0.8545 (t) cc_final: 0.8223 (m) REVERT: D 23 THR cc_start: 0.7783 (m) cc_final: 0.7225 (p) REVERT: D 29 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.6379 (mtt-85) REVERT: E 26 THR cc_start: 0.8240 (m) cc_final: 0.7974 (m) REVERT: E 27 ASN cc_start: 0.6870 (m-40) cc_final: 0.6580 (m110) REVERT: F 23 THR cc_start: 0.7834 (m) cc_final: 0.7120 (p) REVERT: F 24 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (tt) REVERT: F 27 ASN cc_start: 0.6337 (m-40) cc_final: 0.5677 (m-40) REVERT: F 34 LYS cc_start: 0.7588 (mtmm) cc_final: 0.6998 (ptpt) REVERT: G 23 THR cc_start: 0.8048 (m) cc_final: 0.7554 (p) REVERT: G 24 LEU cc_start: 0.8555 (tp) cc_final: 0.8323 (tt) REVERT: H 23 THR cc_start: 0.7875 (m) cc_final: 0.7516 (p) REVERT: I 23 THR cc_start: 0.7723 (m) cc_final: 0.7305 (p) REVERT: I 24 LEU cc_start: 0.8743 (tp) cc_final: 0.8314 (tt) REVERT: J 23 THR cc_start: 0.7773 (m) cc_final: 0.7377 (p) REVERT: J 24 LEU cc_start: 0.8906 (tp) cc_final: 0.8494 (tt) REVERT: J 27 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6703 (m-40) REVERT: J 34 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7396 (mtmt) outliers start: 37 outliers final: 33 residues processed: 206 average time/residue: 0.1264 time to fit residues: 31.2695 Evaluate side-chains 233 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 chunk 11 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096104 restraints weight = 5843.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098424 restraints weight = 2751.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099868 restraints weight = 1577.886| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3070 Z= 0.128 Angle : 0.648 9.878 4220 Z= 0.336 Chirality : 0.042 0.199 640 Planarity : 0.004 0.047 490 Dihedral : 4.381 15.384 460 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 11.00 % Allowed : 45.00 % Favored : 44.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.22 (0.35), residues: 430 helix: -1.72 (0.25), residues: 340 sheet: None (None), residues: 0 loop : -3.00 (0.43), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 32 TYR 0.006 0.001 TYR G 6 ARG 0.009 0.002 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 210) hydrogen bonds : angle 4.13440 ( 630) covalent geometry : bond 0.00282 ( 3070) covalent geometry : angle 0.64800 ( 4220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.7961 (m) cc_final: 0.7712 (p) REVERT: A 18 VAL cc_start: 0.8980 (t) cc_final: 0.8729 (m) REVERT: A 23 THR cc_start: 0.7965 (m) cc_final: 0.7562 (p) REVERT: B 23 THR cc_start: 0.7802 (m) cc_final: 0.7433 (p) REVERT: B 34 LYS cc_start: 0.7589 (mtmm) cc_final: 0.6862 (ptpt) REVERT: C 23 THR cc_start: 0.7859 (m) cc_final: 0.7372 (p) REVERT: C 24 LEU cc_start: 0.8316 (tp) cc_final: 0.7285 (mm) REVERT: D 18 VAL cc_start: 0.8423 (t) cc_final: 0.8170 (m) REVERT: D 23 THR cc_start: 0.7727 (m) cc_final: 0.7163 (p) REVERT: D 24 LEU cc_start: 0.8448 (tp) cc_final: 0.7465 (mm) REVERT: D 29 ARG cc_start: 0.6512 (mtm-85) cc_final: 0.6299 (mtt-85) REVERT: E 23 THR cc_start: 0.7941 (m) cc_final: 0.7343 (p) REVERT: E 26 THR cc_start: 0.8244 (m) cc_final: 0.7983 (m) REVERT: E 27 ASN cc_start: 0.6874 (m-40) cc_final: 0.6588 (m110) REVERT: F 23 THR cc_start: 0.7677 (m) cc_final: 0.6962 (p) REVERT: F 27 ASN cc_start: 0.6273 (m-40) cc_final: 0.5654 (m-40) REVERT: F 34 LYS cc_start: 0.7446 (mtmm) cc_final: 0.6853 (ptpt) REVERT: G 23 THR cc_start: 0.7977 (m) cc_final: 0.7520 (p) REVERT: G 24 LEU cc_start: 0.8495 (tp) cc_final: 0.8289 (tt) REVERT: H 23 THR cc_start: 0.7888 (m) cc_final: 0.7537 (p) REVERT: I 23 THR cc_start: 0.7660 (m) cc_final: 0.7249 (p) REVERT: I 24 LEU cc_start: 0.8765 (tp) cc_final: 0.8344 (tt) REVERT: J 23 THR cc_start: 0.7736 (m) cc_final: 0.7492 (p) REVERT: J 24 LEU cc_start: 0.8904 (tp) cc_final: 0.8514 (tt) REVERT: J 27 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6823 (m-40) REVERT: J 34 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7376 (mtmt) outliers start: 33 outliers final: 30 residues processed: 205 average time/residue: 0.1342 time to fit residues: 33.0461 Evaluate side-chains 227 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095384 restraints weight = 5853.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097724 restraints weight = 2769.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099167 restraints weight = 1611.105| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3070 Z= 0.136 Angle : 0.642 9.944 4220 Z= 0.334 Chirality : 0.043 0.192 640 Planarity : 0.004 0.054 490 Dihedral : 4.369 14.756 460 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 10.67 % Allowed : 44.00 % Favored : 45.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.35), residues: 430 helix: -1.73 (0.25), residues: 340 sheet: None (None), residues: 0 loop : -2.86 (0.43), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE E 32 TYR 0.007 0.001 TYR G 6 ARG 0.008 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 210) hydrogen bonds : angle 4.19432 ( 630) covalent geometry : bond 0.00290 ( 3070) covalent geometry : angle 0.64222 ( 4220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.82 seconds wall clock time: 26 minutes 28.74 seconds (1588.74 seconds total)