Starting phenix.real_space_refine on Sun Mar 10 15:37:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_41815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_41815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_41815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_41815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/03_2024/8u1k_41815.pdb" } 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 Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "E" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "F" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "I" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "J" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Time building chain proxies: 2.03, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 612.4 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: 0.72 Time building geometry restraints manager: 1.41 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: 108.49 - 111.59: 1698 111.59 - 114.70: 422 114.70 - 117.80: 325 117.80 - 120.90: 1006 120.90 - 124.01: 769 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 2.440 nonbonded pdb=" O ARG A 29 " pdb=" OG1 THR A 33 " model vdw 2.206 2.440 nonbonded pdb=" O ARG J 29 " pdb=" OG1 THR J 33 " model vdw 2.206 2.440 nonbonded pdb=" O ARG H 29 " pdb=" OG1 THR H 33 " model vdw 2.207 2.440 nonbonded pdb=" O ARG B 29 " pdb=" OG1 THR B 33 " model vdw 2.207 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain '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: 1.500 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: 6.870 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- 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= 0.239 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 0.316 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: 0.1328 time to fit residues: 35.4840 Evaluate side-chains 222 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 0.5980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 ASN J 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3070 Z= 0.139 Angle : 0.500 4.992 4220 Z= 0.278 Chirality : 0.037 0.093 640 Planarity : 0.004 0.033 490 Dihedral : 9.015 59.462 474 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 11.00 % Allowed : 32.00 % Favored : 57.00 % 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: -4.43 (0.32), residues: 430 helix: -2.50 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.78 (0.39), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE J 32 TYR 0.008 0.002 TYR C 6 ARG 0.009 0.001 ARG E 29 *********************** 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 243 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8102 (m) cc_final: 0.7830 (p) REVERT: A 18 VAL cc_start: 0.8689 (t) cc_final: 0.8432 (m) REVERT: A 23 THR cc_start: 0.7824 (m) cc_final: 0.7407 (p) REVERT: A 24 LEU cc_start: 0.8675 (tp) cc_final: 0.8458 (tp) REVERT: B 18 VAL cc_start: 0.8584 (t) cc_final: 0.8255 (m) REVERT: B 23 THR cc_start: 0.7789 (m) cc_final: 0.7266 (p) REVERT: B 24 LEU cc_start: 0.8641 (tp) cc_final: 0.8406 (tp) REVERT: C 23 THR cc_start: 0.7735 (m) cc_final: 0.7244 (p) REVERT: C 28 LEU cc_start: 0.8651 (tp) cc_final: 0.8387 (tt) REVERT: D 18 VAL cc_start: 0.8482 (t) cc_final: 0.8190 (m) REVERT: D 23 THR cc_start: 0.7841 (m) cc_final: 0.7241 (p) REVERT: D 27 ASN cc_start: 0.6834 (m-40) cc_final: 0.6492 (m110) REVERT: E 16 VAL cc_start: 0.8134 (m) cc_final: 0.7890 (m) REVERT: E 18 VAL cc_start: 0.8572 (t) cc_final: 0.8258 (m) REVERT: F 23 THR cc_start: 0.7843 (m) cc_final: 0.7291 (p) REVERT: G 23 THR cc_start: 0.7973 (m) cc_final: 0.7472 (p) REVERT: G 24 LEU cc_start: 0.8728 (tp) cc_final: 0.8399 (tt) REVERT: G 26 THR cc_start: 0.8106 (t) cc_final: 0.7705 (t) REVERT: G 29 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6349 (mtt-85) REVERT: H 23 THR cc_start: 0.7864 (m) cc_final: 0.7431 (p) REVERT: H 24 LEU cc_start: 0.8797 (tp) cc_final: 0.8576 (tp) REVERT: I 23 THR cc_start: 0.7767 (m) cc_final: 0.7275 (p) REVERT: I 24 LEU cc_start: 0.8778 (tp) cc_final: 0.8536 (tp) REVERT: J 18 VAL cc_start: 0.8550 (t) cc_final: 0.8318 (m) REVERT: J 23 THR cc_start: 0.7822 (m) cc_final: 0.7402 (p) REVERT: J 24 LEU cc_start: 0.8844 (tp) cc_final: 0.8452 (tt) REVERT: J 34 LYS cc_start: 0.7488 (mtmm) cc_final: 0.7177 (mtmm) outliers start: 33 outliers final: 27 residues processed: 218 average time/residue: 0.1331 time to fit residues: 34.7361 Evaluate side-chains 236 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain D residue 8 LEU 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 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 8 LEU 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 30 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3070 Z= 0.181 Angle : 0.526 5.747 4220 Z= 0.297 Chirality : 0.039 0.101 640 Planarity : 0.005 0.047 490 Dihedral : 6.759 51.228 468 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 14.00 % Allowed : 34.33 % Favored : 51.67 % 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: -4.43 (0.31), residues: 430 helix: -2.54 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.57 (0.39), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE A 32 TYR 0.005 0.001 TYR E 6 ARG 0.010 0.001 ARG B 29 *********************** 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 256 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8134 (m) cc_final: 0.7845 (p) REVERT: A 23 THR cc_start: 0.7920 (m) cc_final: 0.7412 (p) REVERT: B 23 THR cc_start: 0.8029 (m) cc_final: 0.7486 (p) REVERT: B 24 LEU cc_start: 0.8763 (tp) cc_final: 0.8556 (tp) REVERT: B 29 ARG cc_start: 0.6510 (mtt-85) cc_final: 0.6240 (mtt-85) REVERT: C 23 THR cc_start: 0.7805 (m) cc_final: 0.7296 (p) REVERT: D 18 VAL cc_start: 0.8439 (t) cc_final: 0.8092 (m) REVERT: D 23 THR cc_start: 0.7829 (m) cc_final: 0.7215 (p) REVERT: D 27 ASN cc_start: 0.6709 (m-40) cc_final: 0.6460 (m-40) REVERT: E 18 VAL cc_start: 0.8500 (t) cc_final: 0.8171 (m) REVERT: F 23 THR cc_start: 0.7855 (m) cc_final: 0.7230 (p) REVERT: F 27 ASN cc_start: 0.6866 (m-40) cc_final: 0.6402 (m-40) REVERT: F 29 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6575 (mtt-85) REVERT: G 23 THR cc_start: 0.8039 (m) cc_final: 0.7507 (p) REVERT: G 24 LEU cc_start: 0.8740 (tp) cc_final: 0.8386 (tt) REVERT: G 26 THR cc_start: 0.8168 (t) cc_final: 0.7585 (t) REVERT: H 23 THR cc_start: 0.7872 (m) cc_final: 0.7462 (p) REVERT: H 24 LEU cc_start: 0.8854 (tp) cc_final: 0.8598 (tp) REVERT: I 23 THR cc_start: 0.7874 (m) cc_final: 0.7383 (p) REVERT: I 24 LEU cc_start: 0.8818 (tp) cc_final: 0.8552 (tp) REVERT: J 18 VAL cc_start: 0.8529 (t) cc_final: 0.8239 (m) REVERT: J 23 THR cc_start: 0.7846 (m) cc_final: 0.7490 (p) REVERT: J 24 LEU cc_start: 0.8839 (tp) cc_final: 0.8390 (tt) REVERT: J 34 LYS cc_start: 0.7503 (mtmm) cc_final: 0.7285 (mtmt) outliers start: 42 outliers final: 33 residues processed: 220 average time/residue: 0.1227 time to fit residues: 32.4196 Evaluate side-chains 248 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 19 THR 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 19 THR 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 30 THR 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 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 4 ILE 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 12 LEU Chi-restraints excluded: chain J residue 17 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0370 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3070 Z= 0.157 Angle : 0.537 6.673 4220 Z= 0.291 Chirality : 0.038 0.097 640 Planarity : 0.004 0.033 490 Dihedral : 6.442 52.467 468 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 10.67 % Allowed : 37.67 % Favored : 51.67 % 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: -4.11 (0.32), residues: 430 helix: -2.35 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.31 (0.42), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE I 32 TYR 0.007 0.001 TYR D 6 ARG 0.006 0.001 ARG G 29 *********************** 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 238 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8080 (m) cc_final: 0.7807 (p) REVERT: A 18 VAL cc_start: 0.8659 (t) cc_final: 0.8399 (m) REVERT: A 23 THR cc_start: 0.7790 (m) cc_final: 0.7341 (p) REVERT: B 18 VAL cc_start: 0.8630 (t) cc_final: 0.8418 (m) REVERT: B 23 THR cc_start: 0.7966 (m) cc_final: 0.7520 (p) REVERT: B 24 LEU cc_start: 0.8618 (tp) cc_final: 0.7476 (mm) REVERT: C 23 THR cc_start: 0.7705 (m) cc_final: 0.7160 (p) REVERT: D 18 VAL cc_start: 0.8410 (t) cc_final: 0.8109 (m) REVERT: D 23 THR cc_start: 0.7749 (m) cc_final: 0.7159 (p) REVERT: D 24 LEU cc_start: 0.8396 (tp) cc_final: 0.7123 (mm) REVERT: D 34 LYS cc_start: 0.7402 (mtmm) cc_final: 0.7121 (mtmm) REVERT: E 18 VAL cc_start: 0.8437 (t) cc_final: 0.8161 (m) REVERT: E 27 ASN cc_start: 0.7064 (m-40) cc_final: 0.6788 (m110) REVERT: F 23 THR cc_start: 0.7833 (m) cc_final: 0.7393 (p) REVERT: G 23 THR cc_start: 0.7905 (m) cc_final: 0.7379 (p) REVERT: G 24 LEU cc_start: 0.8593 (tp) cc_final: 0.8310 (tt) REVERT: G 26 THR cc_start: 0.7727 (t) cc_final: 0.7464 (m) REVERT: H 23 THR cc_start: 0.7831 (m) cc_final: 0.7422 (p) REVERT: H 24 LEU cc_start: 0.8805 (tp) cc_final: 0.8596 (tp) REVERT: I 23 THR cc_start: 0.7795 (m) cc_final: 0.7325 (p) REVERT: I 24 LEU cc_start: 0.8796 (tp) cc_final: 0.8399 (tt) REVERT: J 23 THR cc_start: 0.7805 (m) cc_final: 0.7449 (p) REVERT: J 24 LEU cc_start: 0.8897 (tp) cc_final: 0.8463 (tt) REVERT: J 34 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7235 (mtmt) outliers start: 32 outliers final: 29 residues processed: 213 average time/residue: 0.1327 time to fit residues: 33.5846 Evaluate side-chains 236 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain B residue 19 THR 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 30 THR Chi-restraints excluded: chain C residue 41 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 D residue 26 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 VAL 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 39 VAL 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 I residue 17 ILE Chi-restraints excluded: chain J residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3070 Z= 0.189 Angle : 0.569 6.083 4220 Z= 0.312 Chirality : 0.040 0.168 640 Planarity : 0.005 0.038 490 Dihedral : 6.434 54.817 468 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 15.00 % Allowed : 35.67 % Favored : 49.33 % 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: -4.16 (0.32), residues: 430 helix: -2.40 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.26 (0.44), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 32 TYR 0.006 0.001 TYR G 6 ARG 0.009 0.002 ARG E 29 *********************** 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 253 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8071 (m) cc_final: 0.7781 (p) REVERT: A 23 THR cc_start: 0.7805 (m) cc_final: 0.7349 (p) REVERT: B 18 VAL cc_start: 0.8589 (t) cc_final: 0.8363 (m) REVERT: B 23 THR cc_start: 0.7918 (m) cc_final: 0.7504 (p) REVERT: B 24 LEU cc_start: 0.8537 (tp) cc_final: 0.7474 (mm) REVERT: C 23 THR cc_start: 0.7762 (m) cc_final: 0.7085 (p) REVERT: C 27 ASN cc_start: 0.6786 (m-40) cc_final: 0.6531 (m-40) REVERT: D 18 VAL cc_start: 0.8416 (t) cc_final: 0.8100 (m) REVERT: D 23 THR cc_start: 0.7852 (m) cc_final: 0.7328 (p) REVERT: D 24 LEU cc_start: 0.8460 (tp) cc_final: 0.8260 (tp) REVERT: D 27 ASN cc_start: 0.6952 (m-40) cc_final: 0.6577 (t0) REVERT: E 18 VAL cc_start: 0.8386 (t) cc_final: 0.8099 (m) REVERT: E 27 ASN cc_start: 0.7134 (m-40) cc_final: 0.6672 (m110) REVERT: F 23 THR cc_start: 0.7887 (m) cc_final: 0.7418 (p) REVERT: G 23 THR cc_start: 0.7954 (m) cc_final: 0.7401 (p) REVERT: G 24 LEU cc_start: 0.8699 (tp) cc_final: 0.8399 (tt) REVERT: G 34 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7330 (mtmm) REVERT: H 23 THR cc_start: 0.7862 (m) cc_final: 0.7446 (p) REVERT: H 24 LEU cc_start: 0.8862 (tp) cc_final: 0.8614 (tp) REVERT: I 23 THR cc_start: 0.7829 (m) cc_final: 0.7375 (p) REVERT: I 24 LEU cc_start: 0.8817 (tp) cc_final: 0.8529 (tp) REVERT: J 23 THR cc_start: 0.7825 (m) cc_final: 0.7446 (p) REVERT: J 24 LEU cc_start: 0.8868 (tp) cc_final: 0.8415 (tt) REVERT: J 34 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7267 (mtmt) outliers start: 45 outliers final: 39 residues processed: 218 average time/residue: 0.1332 time to fit residues: 34.6628 Evaluate side-chains 246 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 19 THR 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 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 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 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 39 VAL 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 17 ILE Chi-restraints excluded: chain J residue 41 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3070 Z= 0.178 Angle : 0.583 5.915 4220 Z= 0.316 Chirality : 0.040 0.133 640 Planarity : 0.005 0.050 490 Dihedral : 6.352 59.004 468 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 14.00 % Allowed : 36.33 % 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: -3.90 (0.33), residues: 430 helix: -2.24 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -3.05 (0.45), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 32 TYR 0.008 0.001 TYR G 6 ARG 0.011 0.002 ARG E 29 *********************** 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 245 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8265 (mt) cc_final: 0.8050 (mt) REVERT: A 16 VAL cc_start: 0.8047 (m) cc_final: 0.7740 (p) REVERT: A 23 THR cc_start: 0.7750 (m) cc_final: 0.7320 (p) REVERT: B 18 VAL cc_start: 0.8612 (t) cc_final: 0.8403 (m) REVERT: B 23 THR cc_start: 0.7901 (m) cc_final: 0.7524 (p) REVERT: B 24 LEU cc_start: 0.8397 (tp) cc_final: 0.7370 (mm) REVERT: C 23 THR cc_start: 0.7735 (m) cc_final: 0.7065 (p) REVERT: C 27 ASN cc_start: 0.6745 (m-40) cc_final: 0.6468 (m-40) REVERT: D 18 VAL cc_start: 0.8428 (t) cc_final: 0.8111 (m) REVERT: D 23 THR cc_start: 0.7804 (m) cc_final: 0.7259 (p) REVERT: D 24 LEU cc_start: 0.8428 (tp) cc_final: 0.7143 (mm) REVERT: D 27 ASN cc_start: 0.6848 (m-40) cc_final: 0.6428 (t0) REVERT: D 34 LYS cc_start: 0.7392 (mtmm) cc_final: 0.7171 (mtmm) REVERT: E 18 VAL cc_start: 0.8407 (t) cc_final: 0.8120 (m) REVERT: E 27 ASN cc_start: 0.6930 (m-40) cc_final: 0.6585 (m110) REVERT: F 23 THR cc_start: 0.7863 (m) cc_final: 0.7385 (p) REVERT: G 23 THR cc_start: 0.7949 (m) cc_final: 0.7394 (p) REVERT: G 24 LEU cc_start: 0.8762 (tp) cc_final: 0.8491 (tt) REVERT: G 34 LYS cc_start: 0.7498 (mtmm) cc_final: 0.7269 (mtmm) REVERT: H 23 THR cc_start: 0.7827 (m) cc_final: 0.7430 (p) REVERT: H 24 LEU cc_start: 0.8852 (tp) cc_final: 0.8593 (tp) REVERT: I 23 THR cc_start: 0.7794 (m) cc_final: 0.7326 (p) REVERT: I 24 LEU cc_start: 0.8826 (tp) cc_final: 0.8434 (tt) REVERT: J 23 THR cc_start: 0.7811 (m) cc_final: 0.7423 (p) REVERT: J 24 LEU cc_start: 0.8887 (tp) cc_final: 0.8410 (tt) REVERT: J 34 LYS cc_start: 0.7453 (mtmm) cc_final: 0.7222 (mtmt) outliers start: 42 outliers final: 37 residues processed: 215 average time/residue: 0.1299 time to fit residues: 33.2500 Evaluate side-chains 240 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 19 THR 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 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 D residue 39 VAL 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 4 ILE 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 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 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 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3070 Z= 0.233 Angle : 0.609 7.409 4220 Z= 0.339 Chirality : 0.041 0.129 640 Planarity : 0.005 0.071 490 Dihedral : 6.064 51.247 466 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 15.00 % Allowed : 37.00 % Favored : 48.00 % 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: -4.09 (0.32), residues: 430 helix: -2.40 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -3.02 (0.45), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR G 6 ARG 0.008 0.002 ARG G 29 *********************** 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 255 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8313 (mt) cc_final: 0.8095 (mt) REVERT: A 16 VAL cc_start: 0.8104 (m) cc_final: 0.7814 (p) REVERT: A 23 THR cc_start: 0.7821 (m) cc_final: 0.7359 (p) REVERT: B 18 VAL cc_start: 0.8591 (t) cc_final: 0.8369 (m) REVERT: B 23 THR cc_start: 0.7973 (m) cc_final: 0.7550 (p) REVERT: C 23 THR cc_start: 0.7818 (m) cc_final: 0.7166 (p) REVERT: C 27 ASN cc_start: 0.6781 (m-40) cc_final: 0.6575 (m-40) REVERT: D 18 VAL cc_start: 0.8420 (t) cc_final: 0.8068 (m) REVERT: D 23 THR cc_start: 0.7882 (m) cc_final: 0.7367 (p) REVERT: D 24 LEU cc_start: 0.8518 (tp) cc_final: 0.8292 (tp) REVERT: D 27 ASN cc_start: 0.6943 (m-40) cc_final: 0.6559 (t0) REVERT: D 34 LYS cc_start: 0.7332 (mtmm) cc_final: 0.7047 (mtmm) REVERT: E 18 VAL cc_start: 0.8257 (t) cc_final: 0.7956 (m) REVERT: E 27 ASN cc_start: 0.7125 (m-40) cc_final: 0.6858 (m110) REVERT: F 22 THR cc_start: 0.8270 (m) cc_final: 0.8061 (p) REVERT: F 23 THR cc_start: 0.7925 (m) cc_final: 0.7190 (p) REVERT: F 27 ASN cc_start: 0.6547 (m-40) cc_final: 0.6122 (m-40) REVERT: F 28 LEU cc_start: 0.8590 (tp) cc_final: 0.8375 (tt) REVERT: G 23 THR cc_start: 0.7988 (m) cc_final: 0.7465 (p) REVERT: G 24 LEU cc_start: 0.8830 (tp) cc_final: 0.8538 (tt) REVERT: H 23 THR cc_start: 0.7904 (m) cc_final: 0.7468 (p) REVERT: H 24 LEU cc_start: 0.8850 (tp) cc_final: 0.8597 (tp) REVERT: I 23 THR cc_start: 0.7875 (m) cc_final: 0.7383 (p) REVERT: I 24 LEU cc_start: 0.8752 (tp) cc_final: 0.8366 (tt) REVERT: J 23 THR cc_start: 0.7834 (m) cc_final: 0.7403 (p) REVERT: J 24 LEU cc_start: 0.8878 (tp) cc_final: 0.8538 (tp) REVERT: J 34 LYS cc_start: 0.7502 (mtmm) cc_final: 0.7260 (mtmt) outliers start: 45 outliers final: 40 residues processed: 220 average time/residue: 0.1330 time to fit residues: 34.9976 Evaluate side-chains 250 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 19 THR 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 30 THR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 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 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 4 ILE 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 4 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 2 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3070 Z= 0.276 Angle : 0.620 5.404 4220 Z= 0.353 Chirality : 0.043 0.115 640 Planarity : 0.006 0.072 490 Dihedral : 5.685 44.122 464 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 13.67 % Allowed : 38.00 % Favored : 48.33 % 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: -4.40 (0.31), residues: 430 helix: -2.66 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -2.93 (0.46), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR G 6 ARG 0.016 0.002 ARG F 29 *********************** 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 249 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8186 (m) cc_final: 0.7884 (p) REVERT: A 23 THR cc_start: 0.7912 (m) cc_final: 0.7411 (p) REVERT: B 18 VAL cc_start: 0.8572 (t) cc_final: 0.8313 (m) REVERT: B 23 THR cc_start: 0.8005 (m) cc_final: 0.7578 (p) REVERT: C 23 THR cc_start: 0.7810 (m) cc_final: 0.7148 (p) REVERT: C 27 ASN cc_start: 0.6846 (m-40) cc_final: 0.6573 (m110) REVERT: D 18 VAL cc_start: 0.8417 (t) cc_final: 0.8052 (m) REVERT: D 23 THR cc_start: 0.7868 (m) cc_final: 0.7266 (p) REVERT: D 24 LEU cc_start: 0.8613 (tp) cc_final: 0.8344 (tp) REVERT: D 27 ASN cc_start: 0.6935 (m-40) cc_final: 0.6622 (t0) REVERT: E 27 ASN cc_start: 0.7083 (m-40) cc_final: 0.6748 (m110) REVERT: F 23 THR cc_start: 0.8048 (m) cc_final: 0.7281 (p) REVERT: F 27 ASN cc_start: 0.6657 (m-40) cc_final: 0.6035 (m-40) REVERT: F 28 LEU cc_start: 0.8531 (tp) cc_final: 0.8325 (tt) REVERT: G 23 THR cc_start: 0.8092 (m) cc_final: 0.7534 (p) REVERT: G 24 LEU cc_start: 0.8812 (tp) cc_final: 0.8497 (tt) REVERT: H 23 THR cc_start: 0.7998 (m) cc_final: 0.7562 (p) REVERT: H 24 LEU cc_start: 0.8865 (tp) cc_final: 0.8614 (tp) REVERT: I 23 THR cc_start: 0.7918 (m) cc_final: 0.7396 (p) REVERT: I 24 LEU cc_start: 0.8808 (tp) cc_final: 0.8522 (tp) REVERT: J 23 THR cc_start: 0.7899 (m) cc_final: 0.7409 (p) REVERT: J 24 LEU cc_start: 0.8856 (tp) cc_final: 0.8551 (tp) REVERT: J 28 LEU cc_start: 0.8719 (tp) cc_final: 0.8494 (tt) REVERT: J 34 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7206 (mtmt) outliers start: 41 outliers final: 38 residues processed: 216 average time/residue: 0.1306 time to fit residues: 34.2828 Evaluate side-chains 244 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 19 THR 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 16 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 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 15 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ILE 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 J residue 2 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 17 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4225 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= 0.197 Angle : 0.639 6.720 4220 Z= 0.346 Chirality : 0.041 0.179 640 Planarity : 0.005 0.061 490 Dihedral : 5.232 44.920 462 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 13.33 % Allowed : 37.67 % 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: -3.86 (0.33), residues: 430 helix: -2.29 (0.24), residues: 340 sheet: None (None), residues: 0 loop : -2.70 (0.48), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE D 32 TYR 0.010 0.001 TYR G 6 ARG 0.011 0.002 ARG D 29 *********************** 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 243 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 203 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8171 (m) cc_final: 0.7872 (p) REVERT: A 23 THR cc_start: 0.7826 (m) cc_final: 0.7375 (p) REVERT: B 18 VAL cc_start: 0.8625 (t) cc_final: 0.8378 (m) REVERT: B 23 THR cc_start: 0.7966 (m) cc_final: 0.7539 (p) REVERT: C 23 THR cc_start: 0.7790 (m) cc_final: 0.7117 (p) REVERT: C 27 ASN cc_start: 0.6793 (m-40) cc_final: 0.6545 (m-40) REVERT: D 18 VAL cc_start: 0.8406 (t) cc_final: 0.8037 (m) REVERT: D 23 THR cc_start: 0.7826 (m) cc_final: 0.7239 (p) REVERT: D 24 LEU cc_start: 0.8483 (tp) cc_final: 0.8269 (tp) REVERT: D 27 ASN cc_start: 0.6800 (m-40) cc_final: 0.6452 (t0) REVERT: E 27 ASN cc_start: 0.7067 (m-40) cc_final: 0.6865 (m110) REVERT: F 23 THR cc_start: 0.8085 (m) cc_final: 0.7467 (p) REVERT: F 27 ASN cc_start: 0.6561 (m-40) cc_final: 0.6340 (m-40) REVERT: F 28 LEU cc_start: 0.8526 (tp) cc_final: 0.8322 (tt) REVERT: G 23 THR cc_start: 0.8113 (m) cc_final: 0.7561 (p) REVERT: G 24 LEU cc_start: 0.8684 (tp) cc_final: 0.8402 (tt) REVERT: H 23 THR cc_start: 0.7953 (m) cc_final: 0.7497 (p) REVERT: H 24 LEU cc_start: 0.8868 (tp) cc_final: 0.8606 (tp) REVERT: I 16 VAL cc_start: 0.7632 (m) cc_final: 0.6730 (m) REVERT: I 23 THR cc_start: 0.7860 (m) cc_final: 0.7334 (p) REVERT: I 24 LEU cc_start: 0.8733 (tp) cc_final: 0.8356 (tt) REVERT: J 23 THR cc_start: 0.7866 (m) cc_final: 0.7397 (p) REVERT: J 24 LEU cc_start: 0.8861 (tp) cc_final: 0.8562 (tp) REVERT: J 28 LEU cc_start: 0.8711 (tp) cc_final: 0.8489 (tt) REVERT: J 34 LYS cc_start: 0.7459 (mtmm) cc_final: 0.7191 (mtmt) outliers start: 40 outliers final: 36 residues processed: 213 average time/residue: 0.1341 time to fit residues: 34.0015 Evaluate side-chains 238 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 19 THR 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 15 VAL Chi-restraints excluded: chain D residue 17 ILE 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 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 13 ILE 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 J residue 2 THR Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3070 Z= 0.378 Angle : 0.747 8.180 4220 Z= 0.417 Chirality : 0.047 0.196 640 Planarity : 0.006 0.076 490 Dihedral : 5.894 42.985 462 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 11.67 % Allowed : 41.33 % 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: -4.79 (0.30), residues: 430 helix: -2.90 (0.21), residues: 330 sheet: None (None), residues: 0 loop : -3.25 (0.47), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE E 32 TYR 0.012 0.002 TYR G 6 ARG 0.012 0.002 ARG F 29 ********************** 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 252 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8264 (m) cc_final: 0.7951 (p) REVERT: A 23 THR cc_start: 0.8004 (m) cc_final: 0.7425 (p) REVERT: A 27 ASN cc_start: 0.7207 (m-40) cc_final: 0.6935 (m-40) REVERT: B 23 THR cc_start: 0.8085 (m) cc_final: 0.7629 (p) REVERT: C 23 THR cc_start: 0.7869 (m) cc_final: 0.7112 (p) REVERT: C 27 ASN cc_start: 0.6896 (m-40) cc_final: 0.6473 (m110) REVERT: D 18 VAL cc_start: 0.8359 (t) cc_final: 0.8027 (m) REVERT: D 23 THR cc_start: 0.7960 (m) cc_final: 0.7265 (p) REVERT: D 24 LEU cc_start: 0.8725 (tp) cc_final: 0.8480 (tp) REVERT: D 27 ASN cc_start: 0.7172 (m-40) cc_final: 0.6779 (m-40) REVERT: E 27 ASN cc_start: 0.7240 (m-40) cc_final: 0.6991 (m110) REVERT: F 23 THR cc_start: 0.8089 (m) cc_final: 0.7548 (p) REVERT: F 24 LEU cc_start: 0.8659 (tp) cc_final: 0.8404 (tt) REVERT: F 27 ASN cc_start: 0.6653 (m-40) cc_final: 0.6303 (m-40) REVERT: F 28 LEU cc_start: 0.8701 (tp) cc_final: 0.8372 (tt) REVERT: G 23 THR cc_start: 0.8142 (m) cc_final: 0.7589 (p) REVERT: G 24 LEU cc_start: 0.8885 (tp) cc_final: 0.8535 (tt) REVERT: H 23 THR cc_start: 0.8024 (m) cc_final: 0.7395 (p) REVERT: H 24 LEU cc_start: 0.8882 (tp) cc_final: 0.8590 (tp) REVERT: H 27 ASN cc_start: 0.7485 (m-40) cc_final: 0.7137 (m110) REVERT: I 16 VAL cc_start: 0.7599 (m) cc_final: 0.6398 (p) REVERT: I 23 THR cc_start: 0.7859 (m) cc_final: 0.7201 (p) REVERT: I 24 LEU cc_start: 0.8794 (tp) cc_final: 0.8487 (tp) REVERT: J 23 THR cc_start: 0.7980 (m) cc_final: 0.7269 (p) REVERT: J 24 LEU cc_start: 0.8841 (tp) cc_final: 0.8510 (tp) REVERT: J 27 ASN cc_start: 0.7279 (m110) cc_final: 0.6923 (m110) REVERT: J 28 LEU cc_start: 0.8678 (tp) cc_final: 0.8451 (tt) REVERT: J 34 LYS cc_start: 0.7490 (mtmm) cc_final: 0.7222 (mtmt) outliers start: 35 outliers final: 34 residues processed: 223 average time/residue: 0.1217 time to fit residues: 32.5633 Evaluate side-chains 247 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 19 THR 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 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 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 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 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 2 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 17 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.102232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091789 restraints weight = 5710.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094162 restraints weight = 2772.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095646 restraints weight = 1642.428| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4392 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= 0.215 Angle : 0.689 9.050 4220 Z= 0.364 Chirality : 0.043 0.165 640 Planarity : 0.005 0.042 490 Dihedral : 4.917 18.018 460 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 11.67 % Allowed : 41.33 % 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: -4.17 (0.32), residues: 430 helix: -2.52 (0.23), residues: 340 sheet: None (None), residues: 0 loop : -2.74 (0.49), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 32 TYR 0.009 0.001 TYR G 6 ARG 0.010 0.001 ARG E 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1194.18 seconds wall clock time: 22 minutes 4.51 seconds (1324.51 seconds total)