Starting phenix.real_space_refine on Fri Mar 14 00:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.map" model { file = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x57_33010/03_2025/7x57_33010.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 20 5.16 5 C 5373 2.51 5 N 1845 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.54, per 1000 atoms: 0.57 Number of scatterers: 9767 At special positions: 0 Unit cell: (120.75, 93.45, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 242 15.00 O 2287 8.00 N 1845 7.00 C 5373 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: 2.54 Conformation dependent library (CDL) restraints added in 515.3 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 78.8% alpha, 2.0% beta 120 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.798A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.517A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.559A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.720A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.812A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 118 through 119 358 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 3371 1.45 - 1.57: 4658 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10418 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG LYS H 77 " pdb=" CD LYS H 77 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB MET B 84 " pdb=" CG MET B 84 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 14651 1.76 - 3.53: 407 3.53 - 5.29: 23 5.29 - 7.06: 3 7.06 - 8.82: 2 Bond angle restraints: 15086 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 104.00 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA ARG H 92 " pdb=" CB ARG H 92 " pdb=" CG ARG H 92 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 angle pdb=" C ALA F 76 " pdb=" N LYS F 77 " pdb=" CA LYS F 77 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.35e+00 angle pdb=" C TYR D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 120.28 116.66 3.62 1.34e+00 5.57e-01 7.31e+00 angle pdb=" N GLY D 56 " pdb=" CA GLY D 56 " pdb=" C GLY D 56 " ideal model delta sigma weight residual 112.50 109.51 2.99 1.16e+00 7.43e-01 6.62e+00 ... (remaining 15081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 4448 34.68 - 69.35: 1165 69.35 - 104.02: 32 104.02 - 138.70: 1 138.70 - 173.37: 3 Dihedral angle restraints: 5649 sinusoidal: 3920 harmonic: 1729 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 46.63 173.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 49.06 170.94 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 50.32 169.68 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 300 0.072 - 0.108: 78 0.108 - 0.143: 14 0.143 - 0.179: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CB VAL H 70 " pdb=" CA VAL H 70 " pdb=" CG1 VAL H 70 " pdb=" CG2 VAL H 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA LYS H 77 " pdb=" N LYS H 77 " pdb=" C LYS H 77 " pdb=" CB LYS H 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB ILE F 50 " pdb=" CA ILE F 50 " pdb=" CG1 ILE F 50 " pdb=" CG2 ILE F 50 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1720 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 67 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG B 67 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG B 67 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP B 68 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 49 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C LEU D 49 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU D 49 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 50 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 67 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ARG D 67 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG D 67 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.022 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2199 2.81 - 3.33: 9187 3.33 - 3.85: 19761 3.85 - 4.38: 21986 4.38 - 4.90: 30534 Nonbonded interactions: 83667 Sorted by model distance: nonbonded pdb=" NE2 GLN A 125 " pdb=" OE2 GLU B 53 " model vdw 2.286 3.120 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DC I 39 " model vdw 2.322 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.337 3.120 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.369 3.120 nonbonded pdb=" N SER A 86 " pdb=" OP1 DT J 7 " model vdw 2.375 3.120 ... (remaining 83662 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' selection = (chain 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } 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: 0.310 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.045 10418 Z= 0.196 Angle : 0.633 8.819 15086 Z= 0.411 Chirality : 0.034 0.179 1723 Planarity : 0.007 0.061 1072 Dihedral : 28.743 173.373 4523 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % 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: 0.39 (0.29), residues: 579 helix: 0.79 (0.21), residues: 459 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 75 PHE 0.016 0.001 PHE C 84 TYR 0.017 0.001 TYR B 88 ARG 0.011 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8582 (t) cc_final: 0.8232 (m) REVERT: E 64 LYS cc_start: 0.8483 (tptt) cc_final: 0.8135 (tptm) REVERT: F 55 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7792 (mtt180) REVERT: G 86 SER cc_start: 0.8605 (t) cc_final: 0.8132 (p) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3954 time to fit residues: 85.2416 Evaluate side-chains 118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 93 GLN E 125 GLN G 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.163967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116563 restraints weight = 19672.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.119968 restraints weight = 11297.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.122200 restraints weight = 8296.133| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10418 Z= 0.394 Angle : 0.695 7.655 15086 Z= 0.394 Chirality : 0.037 0.134 1723 Planarity : 0.005 0.041 1072 Dihedral : 32.474 172.980 3289 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.15 % Allowed : 13.47 % Favored : 81.39 % 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: 1.43 (0.33), residues: 579 helix: 1.57 (0.23), residues: 471 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS H 75 PHE 0.017 0.002 PHE A 78 TYR 0.016 0.002 TYR B 88 ARG 0.007 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8598 (t) cc_final: 0.8380 (p) REVERT: A 87 SER cc_start: 0.9123 (m) cc_final: 0.8785 (t) REVERT: A 120 MET cc_start: 0.7392 (mmm) cc_final: 0.7186 (mtt) REVERT: F 44 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8294 (mttp) REVERT: G 86 SER cc_start: 0.8773 (t) cc_final: 0.8370 (p) REVERT: G 112 ILE cc_start: 0.9154 (tp) cc_final: 0.8875 (tp) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.3151 time to fit residues: 63.0000 Evaluate side-chains 139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 125 GLN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.166222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123105 restraints weight = 19113.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.125524 restraints weight = 13415.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126209 restraints weight = 10805.273| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10418 Z= 0.190 Angle : 0.574 6.007 15086 Z= 0.340 Chirality : 0.033 0.137 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.228 173.969 3289 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.38 % Allowed : 18.22 % Favored : 79.41 % 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: 2.39 (0.34), residues: 579 helix: 2.33 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.018 0.001 PHE E 67 TYR 0.010 0.001 TYR F 88 ARG 0.005 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8567 (t) cc_final: 0.8321 (p) REVERT: A 90 MET cc_start: 0.7780 (tpp) cc_final: 0.7404 (mpp) REVERT: F 40 ARG cc_start: 0.8382 (mtp180) cc_final: 0.8118 (ttp-170) REVERT: G 86 SER cc_start: 0.8506 (t) cc_final: 0.8204 (p) REVERT: G 112 ILE cc_start: 0.9139 (tp) cc_final: 0.8861 (tp) outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.2921 time to fit residues: 52.2732 Evaluate side-chains 126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.167999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.127319 restraints weight = 19670.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.128168 restraints weight = 14556.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.128934 restraints weight = 13558.942| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.192 Angle : 0.569 7.586 15086 Z= 0.336 Chirality : 0.033 0.154 1723 Planarity : 0.004 0.030 1072 Dihedral : 32.191 174.247 3289 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.56 % Allowed : 19.60 % Favored : 76.83 % 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: 2.69 (0.34), residues: 579 helix: 2.54 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.015 0.001 PHE C 67 TYR 0.008 0.001 TYR H 72 ARG 0.004 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.600 Fit side-chains REVERT: A 90 MET cc_start: 0.7782 (tpp) cc_final: 0.7405 (mpp) REVERT: D 84 MET cc_start: 0.6842 (ptt) cc_final: 0.6588 (tpp) REVERT: E 73 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: G 86 SER cc_start: 0.8448 (t) cc_final: 0.8208 (p) REVERT: G 112 ILE cc_start: 0.9131 (tp) cc_final: 0.8861 (tp) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.4133 time to fit residues: 73.5688 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.167789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.126423 restraints weight = 19684.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.128491 restraints weight = 13140.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128676 restraints weight = 11811.486| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.204 Angle : 0.579 7.569 15086 Z= 0.339 Chirality : 0.033 0.160 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.164 174.912 3289 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.37 % Allowed : 23.96 % Favored : 72.67 % 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: 2.71 (0.34), residues: 579 helix: 2.56 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.40 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE E 84 TYR 0.008 0.001 TYR B 72 ARG 0.006 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.750 Fit side-chains REVERT: A 90 MET cc_start: 0.7794 (tpp) cc_final: 0.7454 (tpp) REVERT: F 44 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8298 (mmtm) REVERT: G 86 SER cc_start: 0.8457 (t) cc_final: 0.8211 (p) REVERT: G 112 ILE cc_start: 0.9140 (tp) cc_final: 0.8878 (tp) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.3759 time to fit residues: 64.5541 Evaluate side-chains 126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125324 restraints weight = 19811.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.126780 restraints weight = 14473.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127212 restraints weight = 13173.341| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.218 Angle : 0.582 8.192 15086 Z= 0.341 Chirality : 0.034 0.147 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.206 176.353 3289 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.75 % Allowed : 23.17 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.34), residues: 579 helix: 2.52 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.44 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 75 PHE 0.016 0.001 PHE E 67 TYR 0.007 0.001 TYR B 88 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.787 Fit side-chains REVERT: A 90 MET cc_start: 0.7838 (tpp) cc_final: 0.7521 (tpp) REVERT: C 82 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7402 (mt) REVERT: F 84 MET cc_start: 0.6967 (tpp) cc_final: 0.6765 (tpp) REVERT: G 86 SER cc_start: 0.8450 (t) cc_final: 0.8142 (p) REVERT: G 112 ILE cc_start: 0.9145 (tp) cc_final: 0.8891 (tp) outliers start: 24 outliers final: 18 residues processed: 133 average time/residue: 0.2678 time to fit residues: 47.0196 Evaluate side-chains 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.164480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.124554 restraints weight = 19940.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.125563 restraints weight = 16454.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.126617 restraints weight = 15616.531| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10418 Z= 0.319 Angle : 0.643 7.017 15086 Z= 0.369 Chirality : 0.036 0.141 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.553 178.283 3289 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.95 % Allowed : 22.57 % Favored : 72.48 % 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: 2.22 (0.34), residues: 579 helix: 2.25 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.008 0.001 TYR A 99 ARG 0.006 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.690 Fit side-chains REVERT: A 90 MET cc_start: 0.7857 (tpp) cc_final: 0.7590 (tpp) REVERT: B 84 MET cc_start: 0.7543 (tpp) cc_final: 0.7336 (tpp) REVERT: F 44 LYS cc_start: 0.8666 (mmpt) cc_final: 0.8234 (mmtm) REVERT: G 86 SER cc_start: 0.8690 (t) cc_final: 0.8389 (p) REVERT: G 112 ILE cc_start: 0.9194 (tp) cc_final: 0.8958 (tp) outliers start: 25 outliers final: 20 residues processed: 132 average time/residue: 0.2630 time to fit residues: 45.6707 Evaluate side-chains 130 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 125 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.168183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128108 restraints weight = 19954.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.130146 restraints weight = 13503.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.130292 restraints weight = 12369.071| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.199 Angle : 0.591 9.728 15086 Z= 0.345 Chirality : 0.033 0.139 1723 Planarity : 0.004 0.034 1072 Dihedral : 32.207 179.283 3289 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 25.54 % Favored : 70.69 % 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: 2.63 (0.34), residues: 579 helix: 2.53 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.010 0.001 PHE E 67 TYR 0.007 0.001 TYR H 72 ARG 0.005 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.755 Fit side-chains REVERT: A 90 MET cc_start: 0.7723 (tpp) cc_final: 0.7500 (tpp) REVERT: C 61 LEU cc_start: 0.7823 (mp) cc_final: 0.7562 (mp) REVERT: C 82 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7388 (mt) REVERT: F 27 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8362 (mm-40) REVERT: G 86 SER cc_start: 0.8454 (t) cc_final: 0.8215 (p) REVERT: G 112 ILE cc_start: 0.9160 (tp) cc_final: 0.8888 (tp) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.2727 time to fit residues: 46.8526 Evaluate side-chains 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.167657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.128254 restraints weight = 20173.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.130363 restraints weight = 13920.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.130827 restraints weight = 14218.222| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10418 Z= 0.218 Angle : 0.614 10.408 15086 Z= 0.351 Chirality : 0.034 0.150 1723 Planarity : 0.003 0.032 1072 Dihedral : 32.203 178.738 3289 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.76 % Allowed : 25.94 % Favored : 70.30 % 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: 2.55 (0.34), residues: 579 helix: 2.48 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR D 88 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.745 Fit side-chains REVERT: B 84 MET cc_start: 0.7418 (tpp) cc_final: 0.7099 (tpp) REVERT: C 76 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7999 (pp30) REVERT: C 82 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7228 (mm) REVERT: D 84 MET cc_start: 0.6758 (tpp) cc_final: 0.6445 (tpp) REVERT: G 86 SER cc_start: 0.8436 (t) cc_final: 0.8231 (p) REVERT: G 112 ILE cc_start: 0.9152 (tp) cc_final: 0.8894 (tp) outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.2533 time to fit residues: 40.7316 Evaluate side-chains 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.167605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.128296 restraints weight = 20034.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.130764 restraints weight = 13877.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.131147 restraints weight = 13584.291| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 0.045 10418 Z= 0.221 Angle : 0.613 10.838 15086 Z= 0.352 Chirality : 0.033 0.150 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.148 178.627 3289 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.96 % Allowed : 26.34 % Favored : 69.70 % 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: 2.57 (0.35), residues: 579 helix: 2.51 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.77 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.009 0.001 PHE C 67 TYR 0.014 0.001 TYR F 88 ARG 0.004 0.000 ARG H 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.709 Fit side-chains REVERT: B 84 MET cc_start: 0.7422 (tpp) cc_final: 0.6914 (tpp) REVERT: C 76 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7862 (pp30) REVERT: C 82 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7320 (mm) REVERT: D 84 MET cc_start: 0.6728 (tpp) cc_final: 0.6388 (tpp) REVERT: F 44 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8194 (mmtm) REVERT: G 112 ILE cc_start: 0.9163 (tp) cc_final: 0.8900 (tp) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.2596 time to fit residues: 42.0340 Evaluate side-chains 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113358 restraints weight = 19185.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.116928 restraints weight = 12325.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117157 restraints weight = 10486.451| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10418 Z= 0.445 Angle : 0.737 10.514 15086 Z= 0.413 Chirality : 0.039 0.147 1723 Planarity : 0.005 0.042 1072 Dihedral : 32.862 178.243 3289 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.96 % Allowed : 26.14 % Favored : 69.90 % 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: 1.79 (0.34), residues: 579 helix: 2.02 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -2.31 (0.43), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 75 PHE 0.027 0.003 PHE C 67 TYR 0.015 0.002 TYR F 88 ARG 0.009 0.001 ARG F 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2767.08 seconds wall clock time: 50 minutes 17.25 seconds (3017.25 seconds total)