Starting phenix.real_space_refine on Wed Mar 5 15:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.map" model { file = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7h_23212/03_2025/7l7h_23212.cif" } resolution = 4.0 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= 0.005 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 1518 2.51 5 N 424 2.21 5 O 488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2430 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 302 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Time building chain proxies: 1.85, per 1000 atoms: 0.76 Number of scatterers: 2430 At special positions: 0 Unit cell: (101.65, 82.39, 40.66, 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 488 8.00 N 424 7.00 C 1518 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: 0.54 Conformation dependent library (CDL) restraints added in 301.9 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 592 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.461A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.443A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.830A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.513A pdb=" N TYR F 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 48 through 49 removed outlier: 6.402A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL F 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 57 removed outlier: 3.639A pdb=" N THR H 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.755A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 7 hydrogen bonds defined for protein. 21 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: 0.43 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 424 1.29 - 1.36: 392 1.36 - 1.43: 117 1.43 - 1.50: 507 1.50 - 1.58: 998 Bond restraints: 2438 Sorted by residual: bond pdb=" CA THR D 54 " pdb=" CB THR D 54 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.53e-02 4.27e+03 1.40e+01 bond pdb=" CB THR D 44 " pdb=" CG2 THR D 44 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.89e+00 bond pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.55e+00 bond pdb=" CA THR F 44 " pdb=" CB THR F 44 " ideal model delta sigma weight residual 1.534 1.508 0.025 1.45e-02 4.76e+03 3.07e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.97e+00 ... (remaining 2433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 2821 1.86 - 3.72: 390 3.72 - 5.58: 71 5.58 - 7.43: 21 7.43 - 9.29: 6 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N LYS B 60 " pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 114.04 107.66 6.38 1.24e+00 6.50e-01 2.65e+01 angle pdb=" N ALA A 78 " pdb=" CA ALA A 78 " pdb=" C ALA A 78 " ideal model delta sigma weight residual 110.42 117.53 -7.11 1.46e+00 4.69e-01 2.37e+01 angle pdb=" C VAL B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta sigma weight residual 121.31 128.32 -7.01 1.49e+00 4.50e-01 2.21e+01 angle pdb=" N ALA E 78 " pdb=" CA ALA E 78 " pdb=" C ALA E 78 " ideal model delta sigma weight residual 110.42 116.94 -6.52 1.46e+00 4.69e-01 2.00e+01 angle pdb=" N VAL H 77 " pdb=" CA VAL H 77 " pdb=" C VAL H 77 " ideal model delta sigma weight residual 112.17 107.93 4.24 9.50e-01 1.11e+00 1.99e+01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1220 17.23 - 34.46: 156 34.46 - 51.69: 29 51.69 - 68.92: 1 68.92 - 86.14: 1 Dihedral angle restraints: 1407 sinusoidal: 463 harmonic: 944 Sorted by residual: dihedral pdb=" CA VAL A 37 " pdb=" C VAL A 37 " pdb=" N LEU A 38 " pdb=" CA LEU A 38 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY G 68 " pdb=" C GLY G 68 " pdb=" N ALA G 69 " pdb=" CA ALA G 69 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 1404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 200 0.051 - 0.102: 158 0.102 - 0.153: 69 0.153 - 0.204: 17 0.204 - 0.255: 3 Chirality restraints: 447 Sorted by residual: chirality pdb=" CB VAL E 71 " pdb=" CA VAL E 71 " pdb=" CG1 VAL E 71 " pdb=" CG2 VAL E 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB VAL H 40 " pdb=" CA VAL H 40 " pdb=" CG1 VAL H 40 " pdb=" CG2 VAL H 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR C 44 " pdb=" CA THR C 44 " pdb=" OG1 THR C 44 " pdb=" CG2 THR C 44 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 444 not shown) Planarity restraints: 408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " 0.025 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR F 39 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 44 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C THR B 44 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 44 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 45 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 52 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C VAL F 52 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL F 52 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA F 53 " 0.012 2.00e-02 2.50e+03 ... (remaining 405 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 319 2.74 - 3.28: 2220 3.28 - 3.82: 3663 3.82 - 4.36: 3947 4.36 - 4.90: 7666 Nonbonded interactions: 17815 Sorted by model distance: nonbonded pdb=" OG1 THR A 44 " pdb=" O GLU A 46 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR B 44 " pdb=" O GLU B 46 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR H 44 " pdb=" O GLU H 46 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR G 44 " pdb=" O GLU G 46 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR D 44 " pdb=" O GLU D 46 " model vdw 2.286 3.040 ... (remaining 17810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'B' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'C' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'D' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'E' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'F' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = chain 'G' selection = (chain 'H' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) } 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 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 : 0.008 0.073 2438 Z= 0.542 Angle : 1.471 9.292 3309 Z= 0.882 Chirality : 0.079 0.255 447 Planarity : 0.006 0.021 408 Dihedral : 15.099 86.144 815 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.31 % Favored : 63.69 % Rotamer: Outliers : 3.53 % Allowed : 17.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.00 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 50 TYR 0.037 0.006 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.284 Fit side-chains REVERT: A 39 TYR cc_start: 0.5199 (t80) cc_final: 0.4885 (t80) REVERT: A 45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7992 (mptt) REVERT: A 57 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7576 (mp0) REVERT: B 39 TYR cc_start: 0.6141 (m-80) cc_final: 0.5798 (m-80) REVERT: B 57 GLU cc_start: 0.7606 (tt0) cc_final: 0.7280 (tt0) REVERT: B 62 GLN cc_start: 0.7537 (mt0) cc_final: 0.7328 (mp10) REVERT: C 45 LYS cc_start: 0.7943 (tttt) cc_final: 0.7654 (mttp) REVERT: C 57 GLU cc_start: 0.7546 (tt0) cc_final: 0.6735 (tm-30) REVERT: C 62 GLN cc_start: 0.8055 (mp10) cc_final: 0.7715 (mp10) REVERT: C 65 ASN cc_start: 0.6956 (m-40) cc_final: 0.6148 (t0) REVERT: D 57 GLU cc_start: 0.7576 (tt0) cc_final: 0.7180 (tm-30) REVERT: E 43 LYS cc_start: 0.6426 (ttmt) cc_final: 0.5756 (tttp) REVERT: F 45 LYS cc_start: 0.7892 (tttt) cc_final: 0.7668 (mttt) REVERT: F 58 LYS cc_start: 0.5783 (mttt) cc_final: 0.5209 (tptp) outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.1718 time to fit residues: 18.5924 Evaluate side-chains 70 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.101575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.089574 restraints weight = 6050.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.091312 restraints weight = 3754.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.092583 restraints weight = 2630.456| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2438 Z= 0.299 Angle : 0.931 7.435 3309 Z= 0.515 Chirality : 0.059 0.147 447 Planarity : 0.004 0.013 408 Dihedral : 9.283 47.501 360 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.70 % Favored : 75.30 % Rotamer: Outliers : 7.84 % Allowed : 26.67 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.62 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 TYR 0.030 0.005 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.5410 (t80) cc_final: 0.4903 (t80) REVERT: A 45 LYS cc_start: 0.8309 (tttt) cc_final: 0.8006 (mptt) REVERT: C 57 GLU cc_start: 0.7655 (tt0) cc_final: 0.7417 (tm-30) REVERT: C 65 ASN cc_start: 0.7574 (m-40) cc_final: 0.6666 (t0) REVERT: F 58 LYS cc_start: 0.6302 (mttt) cc_final: 0.5460 (tptp) REVERT: F 62 GLN cc_start: 0.7728 (mp10) cc_final: 0.7424 (mp10) outliers start: 20 outliers final: 17 residues processed: 74 average time/residue: 0.1452 time to fit residues: 12.6188 Evaluate side-chains 66 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.103223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.090806 restraints weight = 5783.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.092707 restraints weight = 3547.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.094090 restraints weight = 2447.707| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2438 Z= 0.193 Angle : 0.783 5.808 3309 Z= 0.432 Chirality : 0.055 0.149 447 Planarity : 0.003 0.015 408 Dihedral : 7.946 56.965 359 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.92 % Favored : 77.08 % Rotamer: Outliers : 8.63 % Allowed : 25.88 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.20 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 TYR 0.017 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7208 (mt) REVERT: A 39 TYR cc_start: 0.5236 (t80) cc_final: 0.4700 (t80) REVERT: A 45 LYS cc_start: 0.8371 (tttt) cc_final: 0.7858 (mptt) REVERT: B 57 GLU cc_start: 0.7526 (tt0) cc_final: 0.7319 (tt0) REVERT: C 57 GLU cc_start: 0.7355 (tt0) cc_final: 0.7118 (tm-30) REVERT: C 65 ASN cc_start: 0.7622 (m-40) cc_final: 0.6792 (t0) REVERT: D 62 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 45 LYS cc_start: 0.8414 (mttt) cc_final: 0.8181 (mttm) REVERT: E 50 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4768 (m90) REVERT: G 62 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7893 (tm-30) REVERT: H 38 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6894 (tt) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.1354 time to fit residues: 12.0882 Evaluate side-chains 67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.101118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.089312 restraints weight = 6020.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.091037 restraints weight = 3782.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.092270 restraints weight = 2661.555| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2438 Z= 0.236 Angle : 0.801 6.190 3309 Z= 0.445 Chirality : 0.056 0.177 447 Planarity : 0.003 0.012 408 Dihedral : 8.048 40.858 358 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.08 % Favored : 72.92 % Rotamer: Outliers : 10.98 % Allowed : 23.92 % Favored : 65.10 % 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: -5.17 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.018 0.003 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 45 LYS cc_start: 0.8386 (tttt) cc_final: 0.7935 (mptt) REVERT: C 57 GLU cc_start: 0.7388 (tt0) cc_final: 0.7153 (tm-30) REVERT: E 50 HIS cc_start: 0.5509 (OUTLIER) cc_final: 0.5011 (m90) REVERT: F 62 GLN cc_start: 0.7850 (mp10) cc_final: 0.7597 (tm-30) REVERT: G 62 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8146 (tm-30) REVERT: H 38 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7157 (tt) outliers start: 28 outliers final: 23 residues processed: 75 average time/residue: 0.1237 time to fit residues: 11.1248 Evaluate side-chains 72 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.096262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.084628 restraints weight = 6390.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.086304 restraints weight = 4017.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.087504 restraints weight = 2853.820| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2438 Z= 0.397 Angle : 0.984 7.308 3309 Z= 0.546 Chirality : 0.062 0.169 447 Planarity : 0.005 0.013 408 Dihedral : 9.632 38.938 358 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.52 % Favored : 65.48 % Rotamer: Outliers : 16.08 % Allowed : 21.57 % Favored : 62.35 % 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: -5.67 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 TYR 0.031 0.005 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 45 time to evaluate : 0.279 Fit side-chains REVERT: A 38 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7224 (tt) REVERT: A 39 TYR cc_start: 0.5266 (t80) cc_final: 0.5034 (t80) REVERT: A 45 LYS cc_start: 0.8397 (tttt) cc_final: 0.8043 (mptt) REVERT: C 57 GLU cc_start: 0.7369 (tt0) cc_final: 0.6970 (tm-30) REVERT: D 57 GLU cc_start: 0.7620 (tt0) cc_final: 0.7162 (tm-30) REVERT: E 50 HIS cc_start: 0.5412 (OUTLIER) cc_final: 0.4904 (m90) REVERT: H 38 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (tp) REVERT: H 60 LYS cc_start: 0.8094 (mttt) cc_final: 0.7603 (mmtm) outliers start: 41 outliers final: 35 residues processed: 78 average time/residue: 0.1208 time to fit residues: 11.4221 Evaluate side-chains 80 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 overall best weight: 1.6140 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.104292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.092339 restraints weight = 5921.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.094136 restraints weight = 3708.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.095368 restraints weight = 2599.420| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2438 Z= 0.167 Angle : 0.743 5.768 3309 Z= 0.410 Chirality : 0.055 0.148 447 Planarity : 0.002 0.011 408 Dihedral : 7.049 27.183 358 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.13 % Favored : 78.87 % Rotamer: Outliers : 9.80 % Allowed : 28.63 % Favored : 61.57 % 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: -5.14 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.281 Fit side-chains REVERT: A 38 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7292 (mt) REVERT: A 45 LYS cc_start: 0.8211 (tttt) cc_final: 0.7772 (mptt) REVERT: D 62 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8076 (tm-30) REVERT: E 50 HIS cc_start: 0.5354 (OUTLIER) cc_final: 0.4805 (m90) REVERT: E 62 GLN cc_start: 0.8808 (mp10) cc_final: 0.8436 (mp10) REVERT: G 62 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8057 (tm-30) REVERT: H 38 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7078 (tt) outliers start: 25 outliers final: 19 residues processed: 75 average time/residue: 0.1337 time to fit residues: 11.9918 Evaluate side-chains 70 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.097893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.086457 restraints weight = 6401.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.088085 restraints weight = 4110.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.089255 restraints weight = 2934.163| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2438 Z= 0.301 Angle : 0.890 6.670 3309 Z= 0.491 Chirality : 0.059 0.143 447 Planarity : 0.004 0.011 408 Dihedral : 8.395 33.259 358 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.25 % Favored : 68.75 % Rotamer: Outliers : 14.12 % Allowed : 25.88 % Favored : 60.00 % 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: -5.36 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.022 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 0.245 Fit side-chains REVERT: A 38 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 45 LYS cc_start: 0.8338 (tttt) cc_final: 0.7964 (mptt) REVERT: H 38 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7247 (tt) outliers start: 36 outliers final: 33 residues processed: 74 average time/residue: 0.1380 time to fit residues: 12.3958 Evaluate side-chains 80 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 0.0010 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.9592 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.100757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.089004 restraints weight = 6170.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.090683 restraints weight = 3907.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.091916 restraints weight = 2773.604| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2438 Z= 0.223 Angle : 0.817 7.531 3309 Z= 0.449 Chirality : 0.056 0.139 447 Planarity : 0.003 0.011 408 Dihedral : 7.585 30.475 358 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Rotamer: Outliers : 13.33 % Allowed : 27.06 % Favored : 59.61 % 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: -5.11 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 TYR 0.016 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.285 Fit side-chains REVERT: A 38 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7207 (mt) REVERT: A 45 LYS cc_start: 0.8255 (tttt) cc_final: 0.7837 (mptt) REVERT: C 58 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5889 (tptp) REVERT: D 62 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 43 LYS cc_start: 0.7018 (ttmt) cc_final: 0.6756 (tttt) REVERT: E 50 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.4832 (m90) REVERT: H 38 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7136 (tt) outliers start: 34 outliers final: 28 residues processed: 82 average time/residue: 0.1286 time to fit residues: 12.5559 Evaluate side-chains 85 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.087150 restraints weight = 6378.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.088878 restraints weight = 3927.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.090130 restraints weight = 2741.994| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2438 Z= 0.298 Angle : 0.896 6.716 3309 Z= 0.496 Chirality : 0.058 0.149 447 Planarity : 0.004 0.019 408 Dihedral : 8.366 32.711 358 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.44 % Favored : 67.56 % Rotamer: Outliers : 14.12 % Allowed : 25.88 % Favored : 60.00 % 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: -5.37 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.022 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 0.253 Fit side-chains REVERT: A 38 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7212 (tt) REVERT: A 45 LYS cc_start: 0.8361 (tttt) cc_final: 0.7928 (mptt) REVERT: D 62 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8105 (tm-30) REVERT: E 43 LYS cc_start: 0.7066 (ttmt) cc_final: 0.6767 (tttt) REVERT: E 50 HIS cc_start: 0.5363 (OUTLIER) cc_final: 0.4841 (m90) REVERT: H 38 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7304 (tp) outliers start: 36 outliers final: 31 residues processed: 77 average time/residue: 0.1219 time to fit residues: 11.2947 Evaluate side-chains 80 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.110878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.099175 restraints weight = 5696.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.101016 restraints weight = 3442.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.102304 restraints weight = 2349.665| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2438 Z= 0.185 Angle : 0.760 8.634 3309 Z= 0.414 Chirality : 0.054 0.140 447 Planarity : 0.003 0.024 408 Dihedral : 5.758 22.710 358 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.15 % Favored : 81.85 % Rotamer: Outliers : 7.06 % Allowed : 33.33 % Favored : 59.61 % 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: -4.78 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 TYR 0.014 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.266 Fit side-chains REVERT: A 45 LYS cc_start: 0.8079 (tttt) cc_final: 0.7573 (mptt) REVERT: C 52 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8213 (m) outliers start: 18 outliers final: 11 residues processed: 63 average time/residue: 0.1223 time to fit residues: 9.4259 Evaluate side-chains 59 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.098838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.087585 restraints weight = 6423.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.089160 restraints weight = 4103.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.090348 restraints weight = 2921.648| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2438 Z= 0.325 Angle : 0.988 9.550 3309 Z= 0.541 Chirality : 0.060 0.148 447 Planarity : 0.004 0.016 408 Dihedral : 7.764 32.435 356 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.27 % Favored : 71.73 % Rotamer: Outliers : 7.45 % Allowed : 33.73 % Favored : 58.82 % 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: -5.07 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 TYR 0.029 0.004 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.37 seconds wall clock time: 21 minutes 26.26 seconds (1286.26 seconds total)