Starting phenix.real_space_refine on Thu Mar 13 01:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu2_28602/03_2025/8eu2_28602_neut.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 218 5.49 5 S 8 5.16 5 C 4769 2.51 5 N 1634 2.21 5 O 2053 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: 8682 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2240 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2264 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" 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: "M" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "P" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Time building chain proxies: 7.39, per 1000 atoms: 0.85 Number of scatterers: 8682 At special positions: 0 Unit cell: (121.91, 102.705, 106.045, 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 8 16.00 P 218 15.00 O 2053 8.00 N 1634 7.00 C 4769 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: 2.48 Conformation dependent library (CDL) restraints added in 564.5 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 75.4% alpha, 2.7% beta 109 base pairs and 193 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.527A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.579A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.825A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 removed outlier: 3.586A pdb=" N GLY L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.888A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY L 56 " --> pdb=" O GLU L 52 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 46 through 73 Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.586A pdb=" N ASN M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.577A pdb=" N ASN N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 121 removed outlier: 3.656A pdb=" N ALA N 104 " --> pdb=" O PRO N 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 removed outlier: 3.506A pdb=" N VAL O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.571A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.166A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.552A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.486A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.328A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.727A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.577A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119 278 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 193 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1562 1.33 - 1.45: 3155 1.45 - 1.57: 4112 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9282 Sorted by residual: bond pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" CB PRO O 43 " pdb=" CG PRO O 43 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.02e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.35e+00 bond pdb=" CG PRO O 43 " pdb=" CD PRO O 43 " ideal model delta sigma weight residual 1.503 1.564 -0.061 3.40e-02 8.65e+02 3.17e+00 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12875 1.83 - 3.67: 531 3.67 - 5.50: 49 5.50 - 7.33: 13 7.33 - 9.17: 9 Bond angle restraints: 13477 Sorted by residual: angle pdb=" CA PRO O 43 " pdb=" N PRO O 43 " pdb=" CD PRO O 43 " ideal model delta sigma weight residual 112.00 103.66 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" N GLU M 61 " pdb=" CA GLU M 61 " pdb=" CB GLU M 61 " ideal model delta sigma weight residual 110.16 117.49 -7.33 1.48e+00 4.57e-01 2.45e+01 angle pdb=" C ARG L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CG ARG N 96 " pdb=" CD ARG N 96 " pdb=" NE ARG N 96 " ideal model delta sigma weight residual 112.00 119.73 -7.73 2.20e+00 2.07e-01 1.24e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 124.98 -4.78 1.50e+00 4.44e-01 1.02e+01 ... (remaining 13472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3934 34.93 - 69.86: 1057 69.86 - 104.79: 10 104.79 - 139.72: 0 139.72 - 174.65: 2 Dihedral angle restraints: 5003 sinusoidal: 3480 harmonic: 1523 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 34.65 -174.65 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 69.06 150.94 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ILE P 29 " pdb=" C ILE P 29 " pdb=" N THR P 30 " pdb=" CA THR P 30 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1234 0.053 - 0.105: 243 0.105 - 0.158: 48 0.158 - 0.211: 7 0.211 - 0.263: 4 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA GLU M 61 " pdb=" N GLU M 61 " pdb=" C GLU M 61 " pdb=" CB GLU M 61 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU M 115 " pdb=" CB LEU M 115 " pdb=" CD1 LEU M 115 " pdb=" CD2 LEU M 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE M 79 " pdb=" N ILE M 79 " pdb=" C ILE M 79 " pdb=" CB ILE M 79 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1533 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG O 42 " 0.073 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO O 43 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO O 43 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 43 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO M 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 62 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE M 62 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE M 62 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU M 63 " 0.013 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2644 2.88 - 3.39: 7338 3.39 - 3.89: 17030 3.89 - 4.40: 18879 4.40 - 4.90: 26074 Nonbonded interactions: 71965 Sorted by model distance: nonbonded pdb=" ND2 ASN O 108 " pdb=" O GLY P 42 " model vdw 2.381 3.120 nonbonded pdb=" OE1 GLU O 50 " pdb=" NH1 ARG P 39 " model vdw 2.413 3.120 nonbonded pdb=" OE1 GLU O 73 " pdb=" ND2 ASN P 25 " model vdw 2.415 3.120 nonbonded pdb=" OP1 DC I -23 " pdb=" NH1 ARG K 72 " model vdw 2.417 3.120 nonbonded pdb=" OP1 DG J 48 " pdb=" OH TYR N 37 " model vdw 2.428 3.040 ... (remaining 71960 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 'L' and resid 24 through 94) selection = (chain 'P' and resid 24 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 77.220 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.710 Find NCS groups from input model: 0.140 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.005 0.100 9282 Z= 0.279 Angle : 0.823 9.165 13477 Z= 0.475 Chirality : 0.046 0.263 1536 Planarity : 0.009 0.105 944 Dihedral : 28.134 174.646 4017 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.81 (0.33), residues: 512 helix: -0.24 (0.24), residues: 379 sheet: None (None), residues: 0 loop : -1.01 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 31 PHE 0.027 0.003 PHE K 78 TYR 0.014 0.002 TYR P 72 ARG 0.014 0.001 ARG K 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7603 (mtp-110) REVERT: M 77 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7316 (ttp-170) REVERT: N 64 ASN cc_start: 0.8346 (m-40) cc_final: 0.8027 (m-40) REVERT: N 73 GLU cc_start: 0.7708 (tp30) cc_final: 0.7333 (tp30) REVERT: N 112 THR cc_start: 0.8772 (p) cc_final: 0.8506 (t) REVERT: O 70 LEU cc_start: 0.8505 (tp) cc_final: 0.8189 (tm) REVERT: O 116 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7860 (ttp80) REVERT: O 120 MET cc_start: 0.6907 (mtt) cc_final: 0.6515 (mtt) REVERT: O 128 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8293 (mtp180) REVERT: O 130 ILE cc_start: 0.8824 (mm) cc_final: 0.8553 (mt) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 1.4041 time to fit residues: 285.4135 Evaluate side-chains 191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN M 68 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 94 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103769 restraints weight = 15655.647| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.55 r_work: 0.3385 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9282 Z= 0.294 Angle : 0.629 8.283 13477 Z= 0.376 Chirality : 0.037 0.152 1536 Planarity : 0.005 0.066 944 Dihedral : 30.655 172.591 2971 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.97 % Allowed : 18.99 % Favored : 78.03 % 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: 1.41 (0.37), residues: 512 helix: 1.45 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 31 PHE 0.011 0.001 PHE K 104 TYR 0.016 0.001 TYR M 57 ARG 0.005 0.001 ARG O 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 131 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: M 61 GLU cc_start: 0.7936 (mp0) cc_final: 0.7673 (mp0) REVERT: M 64 GLU cc_start: 0.8235 (tp30) cc_final: 0.7760 (tp30) REVERT: M 68 ASN cc_start: 0.8498 (m-40) cc_final: 0.7028 (m-40) REVERT: N 64 ASN cc_start: 0.8808 (m-40) cc_final: 0.8543 (m-40) REVERT: N 73 GLU cc_start: 0.8489 (tp30) cc_final: 0.8245 (tp30) REVERT: O 69 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: O 120 MET cc_start: 0.7941 (mtt) cc_final: 0.7605 (mtm) REVERT: P 84 MET cc_start: 0.7897 (tpt) cc_final: 0.7682 (tpt) outliers start: 13 outliers final: 8 residues processed: 201 average time/residue: 1.5318 time to fit residues: 323.3448 Evaluate side-chains 205 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 31 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 44 optimal weight: 0.0060 chunk 70 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN O 68 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107366 restraints weight = 15832.255| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.56 r_work: 0.3445 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.182 Angle : 0.574 7.814 13477 Z= 0.343 Chirality : 0.034 0.146 1536 Planarity : 0.004 0.063 944 Dihedral : 30.476 174.895 2968 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.20 % Allowed : 24.03 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.37), residues: 512 helix: 2.19 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS N 79 PHE 0.010 0.001 PHE K 78 TYR 0.014 0.001 TYR M 57 ARG 0.007 0.001 ARG M 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 85 GLN cc_start: 0.8296 (mt0) cc_final: 0.8004 (tt0) REVERT: K 106 ASP cc_start: 0.8041 (m-30) cc_final: 0.7595 (m-30) REVERT: K 109 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8447 (tm) REVERT: K 125 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: K 131 ARG cc_start: 0.8702 (ttt180) cc_final: 0.8377 (mtt-85) REVERT: L 92 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8064 (mmm-85) REVERT: M 32 ARG cc_start: 0.8743 (tmm160) cc_final: 0.8528 (ttp80) REVERT: M 61 GLU cc_start: 0.7907 (mp0) cc_final: 0.7585 (mp0) REVERT: M 64 GLU cc_start: 0.8186 (tp30) cc_final: 0.7734 (tp30) REVERT: M 68 ASN cc_start: 0.8370 (m-40) cc_final: 0.7047 (m-40) REVERT: N 39 TYR cc_start: 0.8497 (t80) cc_final: 0.8137 (t80) REVERT: N 43 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8765 (tppp) REVERT: N 64 ASN cc_start: 0.8783 (m-40) cc_final: 0.8501 (m-40) REVERT: O 70 LEU cc_start: 0.8837 (tp) cc_final: 0.8488 (tm) REVERT: O 116 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8354 (ttp80) REVERT: O 120 MET cc_start: 0.7966 (mtt) cc_final: 0.7649 (mtm) REVERT: O 129 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8215 (tmm-80) REVERT: P 84 MET cc_start: 0.7854 (tpt) cc_final: 0.7607 (tpt) outliers start: 14 outliers final: 8 residues processed: 201 average time/residue: 1.4757 time to fit residues: 312.0368 Evaluate side-chains 208 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101814 restraints weight = 15808.807| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.51 r_work: 0.3363 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9282 Z= 0.329 Angle : 0.634 8.730 13477 Z= 0.377 Chirality : 0.039 0.147 1536 Planarity : 0.005 0.060 944 Dihedral : 30.521 168.413 2968 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.03 % Allowed : 25.17 % Favored : 69.79 % 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: 2.33 (0.37), residues: 512 helix: 2.19 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.51 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 31 PHE 0.010 0.001 PHE K 78 TYR 0.009 0.001 TYR M 50 ARG 0.011 0.001 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: K 131 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8439 (mtt-85) REVERT: L 57 VAL cc_start: 0.9270 (m) cc_final: 0.9025 (t) REVERT: L 92 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: M 64 GLU cc_start: 0.8161 (tp30) cc_final: 0.7662 (tp30) REVERT: M 68 ASN cc_start: 0.8443 (m-40) cc_final: 0.7464 (m-40) REVERT: N 39 TYR cc_start: 0.8576 (t80) cc_final: 0.8370 (t80) REVERT: N 64 ASN cc_start: 0.8832 (m-40) cc_final: 0.8584 (m-40) REVERT: O 70 LEU cc_start: 0.8866 (tp) cc_final: 0.8564 (tm) REVERT: O 97 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8099 (mm-30) REVERT: O 116 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8412 (ttp80) REVERT: O 120 MET cc_start: 0.7959 (mtt) cc_final: 0.7618 (mtm) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 1.5662 time to fit residues: 336.5438 Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102727 restraints weight = 15765.692| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.52 r_work: 0.3375 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9282 Z= 0.289 Angle : 0.620 7.135 13477 Z= 0.370 Chirality : 0.037 0.143 1536 Planarity : 0.005 0.057 944 Dihedral : 30.438 170.139 2968 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.03 % Allowed : 26.32 % Favored : 68.65 % 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 (0.37), residues: 512 helix: 2.37 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.50 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.014 0.001 PHE K 78 TYR 0.009 0.001 TYR P 51 ARG 0.010 0.001 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: K 131 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8429 (mtt-85) REVERT: L 92 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7572 (ttm-80) REVERT: M 61 GLU cc_start: 0.8161 (mp0) cc_final: 0.7415 (mp0) REVERT: M 64 GLU cc_start: 0.8134 (tp30) cc_final: 0.7706 (tp30) REVERT: M 68 ASN cc_start: 0.8393 (m-40) cc_final: 0.7558 (m-40) REVERT: N 64 ASN cc_start: 0.8839 (m-40) cc_final: 0.8594 (m-40) REVERT: N 73 GLU cc_start: 0.8524 (tp30) cc_final: 0.7991 (tp30) REVERT: O 90 MET cc_start: 0.8564 (mpp) cc_final: 0.8329 (mmp) REVERT: O 97 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8164 (mm-30) REVERT: O 116 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8435 (ttp80) REVERT: O 120 MET cc_start: 0.7979 (mtt) cc_final: 0.7678 (mtm) outliers start: 22 outliers final: 13 residues processed: 206 average time/residue: 1.4293 time to fit residues: 310.3651 Evaluate side-chains 218 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN L 93 GLN O 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104221 restraints weight = 15514.445| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.51 r_work: 0.3398 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.231 Angle : 0.608 9.314 13477 Z= 0.359 Chirality : 0.036 0.192 1536 Planarity : 0.005 0.062 944 Dihedral : 30.388 171.228 2968 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.81 % Allowed : 28.15 % Favored : 67.05 % 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: 2.67 (0.37), residues: 512 helix: 2.48 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.46 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 31 PHE 0.011 0.001 PHE K 78 TYR 0.015 0.001 TYR P 88 ARG 0.009 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: K 131 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (mtt-85) REVERT: L 92 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7885 (ttm-80) REVERT: M 61 GLU cc_start: 0.8203 (mp0) cc_final: 0.7858 (mp0) REVERT: M 64 GLU cc_start: 0.8110 (tp30) cc_final: 0.7656 (tp30) REVERT: M 68 ASN cc_start: 0.8355 (m-40) cc_final: 0.7486 (m-40) REVERT: N 64 ASN cc_start: 0.8823 (m-40) cc_final: 0.8575 (m-40) REVERT: O 70 LEU cc_start: 0.8885 (tp) cc_final: 0.8520 (tm) REVERT: O 90 MET cc_start: 0.8518 (mpp) cc_final: 0.8276 (mmp) REVERT: O 97 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8143 (mm-30) REVERT: O 120 MET cc_start: 0.7968 (mtt) cc_final: 0.7657 (mtm) REVERT: P 31 LYS cc_start: 0.8988 (tttp) cc_final: 0.8476 (tptp) outliers start: 21 outliers final: 14 residues processed: 204 average time/residue: 1.3762 time to fit residues: 295.2504 Evaluate side-chains 217 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN L 93 GLN O 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.128460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102852 restraints weight = 15872.481| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.51 r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9282 Z= 0.284 Angle : 0.633 11.173 13477 Z= 0.371 Chirality : 0.037 0.165 1536 Planarity : 0.005 0.062 944 Dihedral : 30.381 169.521 2968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.95 % Allowed : 27.46 % Favored : 66.59 % 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 (0.37), residues: 512 helix: 2.42 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.57 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 31 PHE 0.014 0.001 PHE K 78 TYR 0.032 0.002 TYR P 88 ARG 0.010 0.001 ARG M 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: K 125 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: K 131 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8422 (mtt-85) REVERT: L 92 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7887 (ttm-80) REVERT: M 61 GLU cc_start: 0.8214 (mp0) cc_final: 0.7878 (mp0) REVERT: M 64 GLU cc_start: 0.8133 (tp30) cc_final: 0.7775 (tp30) REVERT: M 68 ASN cc_start: 0.8396 (m-40) cc_final: 0.7781 (m-40) REVERT: N 64 ASN cc_start: 0.8825 (m-40) cc_final: 0.8578 (m-40) REVERT: O 70 LEU cc_start: 0.8913 (tp) cc_final: 0.8559 (tm) REVERT: O 90 MET cc_start: 0.8548 (mpp) cc_final: 0.8305 (mmp) REVERT: O 97 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8174 (mm-30) REVERT: O 120 MET cc_start: 0.8034 (mtt) cc_final: 0.7793 (mtp) REVERT: P 31 LYS cc_start: 0.8997 (tttp) cc_final: 0.8465 (tptp) outliers start: 26 outliers final: 19 residues processed: 210 average time/residue: 1.5917 time to fit residues: 350.9282 Evaluate side-chains 226 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 0.0370 chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN L 93 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN P 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104365 restraints weight = 15871.956| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.51 r_work: 0.3403 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9282 Z= 0.235 Angle : 0.625 10.122 13477 Z= 0.363 Chirality : 0.036 0.173 1536 Planarity : 0.005 0.061 944 Dihedral : 30.348 171.121 2968 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.03 % Allowed : 28.83 % Favored : 66.13 % 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 (0.37), residues: 512 helix: 2.51 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.52 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 31 PHE 0.011 0.001 PHE K 78 TYR 0.026 0.002 TYR P 88 ARG 0.009 0.001 ARG M 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.627 Fit side-chains REVERT: K 72 ARG cc_start: 0.8989 (mtt90) cc_final: 0.8756 (mtt180) REVERT: K 125 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: K 131 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (mtt-85) REVERT: L 92 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: M 61 GLU cc_start: 0.8166 (mp0) cc_final: 0.7864 (mp0) REVERT: M 64 GLU cc_start: 0.8084 (tp30) cc_final: 0.7680 (tp30) REVERT: M 68 ASN cc_start: 0.8371 (m-40) cc_final: 0.7499 (m-40) REVERT: N 43 LYS cc_start: 0.9107 (mmtp) cc_final: 0.8895 (tppp) REVERT: N 64 ASN cc_start: 0.8810 (m-40) cc_final: 0.8561 (m-40) REVERT: O 97 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8160 (mm-30) REVERT: O 120 MET cc_start: 0.7997 (mtt) cc_final: 0.7761 (mtp) REVERT: P 31 LYS cc_start: 0.8979 (tttp) cc_final: 0.8454 (tptp) REVERT: P 84 MET cc_start: 0.8182 (tmt) cc_final: 0.7134 (tmt) outliers start: 22 outliers final: 13 residues processed: 203 average time/residue: 1.4788 time to fit residues: 317.8995 Evaluate side-chains 215 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 0.4980 chunk 69 optimal weight: 0.0470 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN L 93 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105123 restraints weight = 15799.965| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.51 r_work: 0.3412 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9282 Z= 0.222 Angle : 0.629 11.011 13477 Z= 0.364 Chirality : 0.035 0.189 1536 Planarity : 0.005 0.061 944 Dihedral : 30.331 171.609 2968 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.12 % Allowed : 30.21 % Favored : 65.68 % 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: 2.70 (0.37), residues: 512 helix: 2.53 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.54 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 31 PHE 0.010 0.001 PHE K 78 TYR 0.031 0.002 TYR P 88 ARG 0.010 0.001 ARG M 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.611 Fit side-chains REVERT: K 72 ARG cc_start: 0.8977 (mtt90) cc_final: 0.8745 (mtt180) REVERT: K 125 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: K 131 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8388 (mtt-85) REVERT: L 45 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7872 (mtp-110) REVERT: L 92 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: M 61 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7874 (mp0) REVERT: M 64 GLU cc_start: 0.8080 (tp30) cc_final: 0.7687 (tp30) REVERT: M 68 ASN cc_start: 0.8358 (m-40) cc_final: 0.7524 (m-40) REVERT: N 43 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8893 (tppp) REVERT: N 64 ASN cc_start: 0.8798 (m-40) cc_final: 0.8545 (m-40) REVERT: O 70 LEU cc_start: 0.8887 (tp) cc_final: 0.8518 (tm) REVERT: O 97 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8131 (mm-30) REVERT: O 120 MET cc_start: 0.7983 (mtt) cc_final: 0.7720 (mtp) REVERT: O 128 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8753 (mtm180) REVERT: P 31 LYS cc_start: 0.8986 (tttp) cc_final: 0.8456 (tptp) REVERT: P 88 TYR cc_start: 0.8270 (m-10) cc_final: 0.8041 (m-10) outliers start: 18 outliers final: 11 residues processed: 204 average time/residue: 1.3655 time to fit residues: 293.1690 Evaluate side-chains 214 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104756 restraints weight = 15735.442| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.50 r_work: 0.3410 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9282 Z= 0.237 Angle : 0.648 11.988 13477 Z= 0.369 Chirality : 0.036 0.217 1536 Planarity : 0.005 0.061 944 Dihedral : 30.314 171.420 2968 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.35 % Allowed : 30.43 % Favored : 65.22 % 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: 2.70 (0.37), residues: 512 helix: 2.56 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.61 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 31 PHE 0.013 0.001 PHE K 78 TYR 0.032 0.002 TYR P 88 ARG 0.011 0.001 ARG M 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8990 (mtt90) cc_final: 0.8753 (mtt180) REVERT: K 125 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: K 131 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8376 (mtt-85) REVERT: L 92 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: M 61 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7910 (mp0) REVERT: M 64 GLU cc_start: 0.8099 (tp30) cc_final: 0.7706 (tp30) REVERT: M 68 ASN cc_start: 0.8358 (m-40) cc_final: 0.7516 (m-40) REVERT: N 43 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8885 (tppp) REVERT: N 64 ASN cc_start: 0.8813 (m-40) cc_final: 0.8566 (m-40) REVERT: O 70 LEU cc_start: 0.8886 (tp) cc_final: 0.8520 (tm) REVERT: O 120 MET cc_start: 0.8012 (mtt) cc_final: 0.7810 (mtp) REVERT: P 31 LYS cc_start: 0.8990 (tttp) cc_final: 0.8453 (tptp) REVERT: P 88 TYR cc_start: 0.8255 (m-10) cc_final: 0.8013 (m-10) outliers start: 19 outliers final: 13 residues processed: 206 average time/residue: 1.4099 time to fit residues: 305.4214 Evaluate side-chains 216 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.0020 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105063 restraints weight = 15878.360| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.51 r_work: 0.3418 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9282 Z= 0.219 Angle : 0.644 12.254 13477 Z= 0.367 Chirality : 0.036 0.218 1536 Planarity : 0.005 0.061 944 Dihedral : 30.318 171.643 2968 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.35 % Allowed : 30.66 % Favored : 64.99 % 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 (0.37), residues: 512 helix: 2.55 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.61 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 31 PHE 0.009 0.001 PHE K 78 TYR 0.026 0.002 TYR P 88 ARG 0.011 0.001 ARG M 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8999.45 seconds wall clock time: 156 minutes 44.12 seconds (9404.12 seconds total)