Starting phenix.real_space_refine on Mon Mar 11 16:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_28602_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_28602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_28602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_28602_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu2_28602/03_2024/8eu2_28602_neut.pdb" } 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 Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.89, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 4.38 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: 3.43 Time building geometry restraints manager: 8.53 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: 98.31 - 105.26: 986 105.26 - 112.21: 5020 112.21 - 119.16: 2683 119.16 - 126.11: 4091 126.11 - 133.06: 697 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 2.520 nonbonded pdb=" OE1 GLU O 50 " pdb=" NH1 ARG P 39 " model vdw 2.413 2.520 nonbonded pdb=" OE1 GLU O 73 " pdb=" ND2 ASN P 25 " model vdw 2.415 2.520 nonbonded pdb=" OP1 DC I -23 " pdb=" NH1 ARG K 72 " model vdw 2.417 2.520 nonbonded pdb=" OP1 DG J 48 " pdb=" OH TYR N 37 " model vdw 2.428 2.440 ... (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 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: 6.070 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: 22.570 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 35.100 Find NCS groups from input model: 0.260 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.430 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.667 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: 1.4073 time to fit residues: 285.7097 Evaluate side-chains 191 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 GLN L 27 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9282 Z= 0.305 Angle : 0.632 7.967 13477 Z= 0.378 Chirality : 0.038 0.148 1536 Planarity : 0.005 0.066 944 Dihedral : 30.648 172.234 2971 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.66 % Allowed : 17.85 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.37), residues: 512 helix: 1.43 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.63 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.011 0.002 PHE K 104 TYR 0.016 0.001 TYR M 57 ARG 0.006 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 215 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8209 (mtt90) REVERT: K 131 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: M 61 GLU cc_start: 0.7169 (mp0) cc_final: 0.6860 (mp0) REVERT: M 64 GLU cc_start: 0.7475 (tp30) cc_final: 0.7170 (tp30) REVERT: M 68 ASN cc_start: 0.8198 (m-40) cc_final: 0.6480 (m-40) REVERT: N 64 ASN cc_start: 0.8313 (m-40) cc_final: 0.7978 (m-40) REVERT: N 73 GLU cc_start: 0.7782 (tp30) cc_final: 0.7535 (tp30) REVERT: O 70 LEU cc_start: 0.8591 (tp) cc_final: 0.8315 (tm) REVERT: O 90 MET cc_start: 0.7733 (mpp) cc_final: 0.7531 (mmt) REVERT: O 92 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8390 (mm) REVERT: O 120 MET cc_start: 0.7039 (mtt) cc_final: 0.6726 (mtm) REVERT: O 130 ILE cc_start: 0.8845 (mm) cc_final: 0.8618 (mt) outliers start: 16 outliers final: 10 residues processed: 202 average time/residue: 1.4612 time to fit residues: 310.1151 Evaluate side-chains 210 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain M residue 59 THR 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 119 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 92 LEU 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 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9282 Z= 0.308 Angle : 0.626 8.049 13477 Z= 0.373 Chirality : 0.038 0.145 1536 Planarity : 0.005 0.060 944 Dihedral : 30.653 170.320 2968 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.35 % Allowed : 24.49 % Favored : 71.17 % 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: 2.01 (0.37), residues: 512 helix: 1.95 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 126 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 0.002 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 216 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8242 (mtt90) REVERT: K 125 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: K 131 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7983 (mtt-85) REVERT: L 57 VAL cc_start: 0.8880 (m) cc_final: 0.8656 (t) REVERT: L 92 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7762 (ttm-80) REVERT: M 61 GLU cc_start: 0.7199 (mp0) cc_final: 0.6840 (mp0) REVERT: M 64 GLU cc_start: 0.7437 (tp30) cc_final: 0.7124 (tp30) REVERT: M 68 ASN cc_start: 0.8075 (m-40) cc_final: 0.6849 (m-40) REVERT: N 64 ASN cc_start: 0.8335 (m-40) cc_final: 0.8009 (m-40) REVERT: O 70 LEU cc_start: 0.8612 (tp) cc_final: 0.8318 (tm) REVERT: O 116 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8028 (ttp80) REVERT: O 120 MET cc_start: 0.6988 (mtt) cc_final: 0.6672 (mtm) outliers start: 19 outliers final: 8 residues processed: 200 average time/residue: 1.4151 time to fit residues: 297.3867 Evaluate side-chains 208 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG 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 86 VAL Chi-restraints excluded: chain L residue 92 ARG 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 75 SER Chi-restraints excluded: chain O residue 57 SER 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 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN P 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9282 Z= 0.302 Angle : 0.622 8.873 13477 Z= 0.371 Chirality : 0.037 0.141 1536 Planarity : 0.005 0.058 944 Dihedral : 30.535 169.506 2968 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.18 % Allowed : 23.80 % Favored : 70.02 % 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: 2.25 (0.37), residues: 512 helix: 2.19 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.69 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.013 0.002 PHE K 78 TYR 0.009 0.001 TYR P 51 ARG 0.009 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 228 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8259 (mtt90) REVERT: K 125 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: K 131 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8002 (mtt-85) REVERT: L 45 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7494 (mtp-110) REVERT: L 57 VAL cc_start: 0.8874 (m) cc_final: 0.8645 (t) REVERT: L 92 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7407 (ttm-80) REVERT: M 64 GLU cc_start: 0.7383 (tp30) cc_final: 0.7085 (tp30) REVERT: M 68 ASN cc_start: 0.8030 (m-40) cc_final: 0.7240 (m-40) REVERT: N 44 GLN cc_start: 0.8496 (tt0) cc_final: 0.8249 (tt0) REVERT: N 64 ASN cc_start: 0.8355 (m-40) cc_final: 0.8046 (m-40) REVERT: N 76 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7572 (mtp180) REVERT: O 70 LEU cc_start: 0.8614 (tp) cc_final: 0.8324 (tm) REVERT: O 72 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8529 (ttm-80) REVERT: O 90 MET cc_start: 0.7739 (mpp) cc_final: 0.7503 (mmp) REVERT: O 97 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7398 (mm-30) REVERT: O 116 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7549 (ttp80) REVERT: O 120 MET cc_start: 0.6981 (mtt) cc_final: 0.6536 (mtt) REVERT: P 31 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8334 (tptm) outliers start: 27 outliers final: 15 residues processed: 204 average time/residue: 1.4988 time to fit residues: 321.4036 Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG 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 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 61 GLU 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 68 GLU Chi-restraints excluded: chain N residue 76 ARG 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 31 LYS Chi-restraints excluded: chain P residue 70 VAL 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 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2181 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= 0.294 Angle : 0.618 7.163 13477 Z= 0.369 Chirality : 0.037 0.178 1536 Planarity : 0.005 0.061 944 Dihedral : 30.508 169.584 2968 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.95 % Allowed : 25.86 % Favored : 68.19 % 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: 2.45 (0.37), residues: 512 helix: 2.36 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.65 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.017 0.002 PHE K 78 TYR 0.008 0.001 TYR P 88 ARG 0.007 0.001 ARG O 63 *********************** 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 230 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8258 (mtt90) REVERT: K 125 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: K 131 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: L 57 VAL cc_start: 0.8884 (m) cc_final: 0.8644 (t) REVERT: L 92 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7584 (ttm-80) REVERT: M 64 GLU cc_start: 0.7377 (tp30) cc_final: 0.7028 (tp30) REVERT: M 68 ASN cc_start: 0.7999 (m-40) cc_final: 0.7005 (m-40) REVERT: N 44 GLN cc_start: 0.8484 (tt0) cc_final: 0.8239 (tt0) REVERT: N 64 ASN cc_start: 0.8353 (m-40) cc_final: 0.8042 (m-40) REVERT: O 70 LEU cc_start: 0.8610 (tp) cc_final: 0.8313 (tm) REVERT: O 97 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7392 (mm-30) REVERT: O 116 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7955 (ttp80) REVERT: O 120 MET cc_start: 0.6983 (mtt) cc_final: 0.6548 (mtm) REVERT: P 31 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8332 (tptm) outliers start: 26 outliers final: 15 residues processed: 206 average time/residue: 1.4864 time to fit residues: 321.1142 Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG 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 86 VAL 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 68 GLU 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 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN M 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9282 Z= 0.278 Angle : 0.620 8.909 13477 Z= 0.368 Chirality : 0.037 0.152 1536 Planarity : 0.005 0.059 944 Dihedral : 30.482 169.873 2968 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.26 % Allowed : 27.23 % Favored : 67.51 % 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: 2.48 (0.37), residues: 512 helix: 2.38 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.63 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.012 0.001 PHE K 78 TYR 0.016 0.002 TYR P 88 ARG 0.006 0.001 ARG M 20 *********************** 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 224 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8248 (mtt90) REVERT: K 125 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: K 131 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: L 92 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7488 (ttm-80) REVERT: M 61 GLU cc_start: 0.7522 (mp0) cc_final: 0.7111 (mp0) REVERT: M 64 GLU cc_start: 0.7364 (tp30) cc_final: 0.7040 (tp30) REVERT: M 68 ASN cc_start: 0.8013 (m-40) cc_final: 0.7105 (m-40) REVERT: N 44 GLN cc_start: 0.8479 (tt0) cc_final: 0.8242 (tt0) REVERT: N 64 ASN cc_start: 0.8351 (m-40) cc_final: 0.8033 (m-40) REVERT: O 97 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7414 (mm-30) REVERT: O 120 MET cc_start: 0.6975 (mtt) cc_final: 0.6655 (mtm) REVERT: P 31 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8336 (tptm) outliers start: 23 outliers final: 14 residues processed: 205 average time/residue: 1.3819 time to fit residues: 298.1164 Evaluate side-chains 217 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG 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 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 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL 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 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2316 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= 0.279 Angle : 0.633 10.907 13477 Z= 0.371 Chirality : 0.037 0.142 1536 Planarity : 0.005 0.058 944 Dihedral : 30.461 169.935 2968 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.49 % Allowed : 28.38 % 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: 2.49 (0.37), residues: 512 helix: 2.40 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.67 (0.50), residues: 131 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 0.030 0.002 TYR P 88 ARG 0.007 0.001 ARG O 63 *********************** 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 226 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8253 (mtt90) REVERT: K 125 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: K 131 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: L 92 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7458 (ttm-80) REVERT: M 61 GLU cc_start: 0.7509 (mp0) cc_final: 0.7102 (mp0) REVERT: M 64 GLU cc_start: 0.7358 (tp30) cc_final: 0.7008 (tp30) REVERT: M 68 ASN cc_start: 0.8000 (m-40) cc_final: 0.7037 (m-40) REVERT: N 44 GLN cc_start: 0.8478 (tt0) cc_final: 0.8240 (tt0) REVERT: N 64 ASN cc_start: 0.8352 (m-40) cc_final: 0.8032 (m-40) REVERT: O 70 LEU cc_start: 0.8688 (tp) cc_final: 0.8239 (tm) REVERT: O 97 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7418 (mm-30) REVERT: O 120 MET cc_start: 0.6968 (mtt) cc_final: 0.6721 (mtp) REVERT: P 31 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8336 (tptm) outliers start: 24 outliers final: 15 residues processed: 206 average time/residue: 1.4436 time to fit residues: 312.4850 Evaluate side-chains 221 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 90 MET 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 33 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 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2336 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= 0.229 Angle : 0.619 10.138 13477 Z= 0.361 Chirality : 0.035 0.137 1536 Planarity : 0.005 0.059 944 Dihedral : 30.395 171.433 2968 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.26 % Allowed : 29.52 % 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: 2.59 (0.37), residues: 512 helix: 2.46 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.65 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 31 PHE 0.012 0.001 PHE K 78 TYR 0.029 0.002 TYR P 88 ARG 0.011 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 227 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.568 Fit side-chains REVERT: K 72 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8193 (mtt180) REVERT: K 125 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: K 131 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7978 (mtt-85) REVERT: L 92 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7381 (ttm-80) REVERT: M 61 GLU cc_start: 0.7488 (mp0) cc_final: 0.7116 (mp0) REVERT: M 64 GLU cc_start: 0.7335 (tp30) cc_final: 0.6976 (tp30) REVERT: M 68 ASN cc_start: 0.7960 (m-40) cc_final: 0.6983 (m-40) REVERT: N 44 GLN cc_start: 0.8477 (tt0) cc_final: 0.8246 (tt0) REVERT: N 64 ASN cc_start: 0.8347 (m-40) cc_final: 0.8037 (m-40) REVERT: O 70 LEU cc_start: 0.8660 (tp) cc_final: 0.8251 (tm) REVERT: O 90 MET cc_start: 0.7716 (mpp) cc_final: 0.7509 (mmp) REVERT: O 97 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7400 (mm-30) REVERT: P 31 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8366 (tptm) REVERT: P 84 MET cc_start: 0.6990 (tmt) cc_final: 0.5484 (tmt) outliers start: 23 outliers final: 12 residues processed: 209 average time/residue: 1.4667 time to fit residues: 322.4830 Evaluate side-chains 219 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 90 MET 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 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 68 GLU Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 70 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN O 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2394 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= 0.265 Angle : 0.652 11.100 13477 Z= 0.374 Chirality : 0.037 0.246 1536 Planarity : 0.005 0.060 944 Dihedral : 30.385 170.481 2968 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.58 % Allowed : 31.12 % Favored : 64.30 % 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: 2.51 (0.37), residues: 512 helix: 2.40 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 113 PHE 0.011 0.001 PHE K 78 TYR 0.037 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 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 0.667 Fit side-chains REVERT: K 72 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8191 (mtt180) REVERT: K 125 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: K 131 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7988 (mtt-85) REVERT: L 45 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7484 (mtp-110) REVERT: L 92 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7468 (ttm-80) REVERT: M 61 GLU cc_start: 0.7488 (mp0) cc_final: 0.7126 (mp0) REVERT: M 64 GLU cc_start: 0.7344 (tp30) cc_final: 0.6992 (tp30) REVERT: M 68 ASN cc_start: 0.7976 (m-40) cc_final: 0.7049 (m-40) REVERT: N 44 GLN cc_start: 0.8476 (tt0) cc_final: 0.8242 (tt0) REVERT: N 64 ASN cc_start: 0.8346 (m-40) cc_final: 0.8035 (m-40) REVERT: O 70 LEU cc_start: 0.8662 (tp) cc_final: 0.8276 (tm) REVERT: O 90 MET cc_start: 0.7721 (mpp) cc_final: 0.7498 (mmp) REVERT: O 97 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7404 (mm-30) REVERT: P 31 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8368 (tptm) outliers start: 20 outliers final: 14 residues processed: 207 average time/residue: 1.3684 time to fit residues: 298.0942 Evaluate side-chains 222 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 90 MET 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 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 68 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL 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 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 108 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9282 Z= 0.296 Angle : 0.668 12.737 13477 Z= 0.383 Chirality : 0.038 0.228 1536 Planarity : 0.005 0.061 944 Dihedral : 30.383 169.468 2968 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.49 % Allowed : 29.75 % Favored : 64.76 % 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: 2.46 (0.37), residues: 512 helix: 2.38 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.70 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 31 PHE 0.013 0.001 PHE K 78 TYR 0.027 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 231 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: K 72 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8262 (mtt90) REVERT: K 125 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: K 131 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8008 (mtt-85) REVERT: L 92 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7479 (ttm-80) REVERT: M 61 GLU cc_start: 0.7494 (mp0) cc_final: 0.7149 (mp0) REVERT: M 64 GLU cc_start: 0.7367 (tp30) cc_final: 0.7032 (tp30) REVERT: M 68 ASN cc_start: 0.8000 (m-40) cc_final: 0.7164 (m-40) REVERT: N 44 GLN cc_start: 0.8477 (tt0) cc_final: 0.8246 (tt0) REVERT: N 64 ASN cc_start: 0.8361 (m-40) cc_final: 0.8054 (m-40) REVERT: O 97 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7429 (mm-30) REVERT: P 31 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8334 (tptm) REVERT: P 84 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6496 (tmt) outliers start: 24 outliers final: 14 residues processed: 212 average time/residue: 1.4541 time to fit residues: 323.7355 Evaluate side-chains 227 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 90 MET 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 33 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 P residue 31 LYS Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 84 MET 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 57 optimal weight: 0.0070 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 chunk 37 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN K 108 ASN K 125 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107761 restraints weight = 15562.598| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.55 r_work: 0.3453 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9282 Z= 0.190 Angle : 0.624 12.446 13477 Z= 0.356 Chirality : 0.035 0.209 1536 Planarity : 0.005 0.066 944 Dihedral : 30.247 174.341 2968 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.43 % Allowed : 32.95 % Favored : 63.62 % 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: 2.79 (0.37), residues: 512 helix: 2.65 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.63 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 31 PHE 0.008 0.001 PHE K 78 TYR 0.019 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: 4974.83 seconds wall clock time: 88 minutes 6.56 seconds (5286.56 seconds total)