Starting phenix.real_space_refine on Sun Dec 29 17:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437.map" model { file = "/net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pii_13437/12_2024/7pii_13437_neut.cif" } resolution = 2.68 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= 0.002 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 244 5.49 5 S 8 5.16 5 C 6321 2.51 5 N 2070 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2506 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2514 Classifications: {'DNA': 123} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 122} Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 7.65, per 1000 atoms: 0.68 Number of scatterers: 11192 At special positions: 0 Unit cell: (80.607, 114.678, 123.819, 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 244 15.00 O 2549 8.00 N 2070 7.00 C 6321 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: 3.08 Conformation dependent library (CDL) restraints added in 700.6 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 68.9% alpha, 2.6% beta 121 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.629A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.618A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 5.628A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 87 through 116 Processing helix chain 'E' and resid 122 through 134 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.479A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.727A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.452A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.916A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.180A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'L' and resid 516 through 517 408 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 282 hydrogen bonds 564 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1668 1.32 - 1.45: 4128 1.45 - 1.57: 5598 1.57 - 1.69: 487 1.69 - 1.81: 14 Bond restraints: 11895 Sorted by residual: bond pdb=" N ILE D 54 " pdb=" CA ILE D 54 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL K 517 " pdb=" CA VAL K 517 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.56e+00 bond pdb=" N VAL K 533 " pdb=" CA VAL K 533 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.22e+00 bond pdb=" N THR K 518 " pdb=" CA THR K 518 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.20e+00 bond pdb=" N VAL K 532 " pdb=" CA VAL K 532 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.24e-02 6.50e+03 8.70e+00 ... (remaining 11890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 16152 1.63 - 3.27: 871 3.27 - 4.90: 83 4.90 - 6.54: 9 6.54 - 8.17: 1 Bond angle restraints: 17116 Sorted by residual: angle pdb=" N LEU F 49 " pdb=" CA LEU F 49 " pdb=" C LEU F 49 " ideal model delta sigma weight residual 113.18 108.67 4.51 1.21e+00 6.83e-01 1.39e+01 angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 113.01 108.59 4.42 1.20e+00 6.94e-01 1.36e+01 angle pdb=" N VAL E 119 " pdb=" CA VAL E 119 " pdb=" C VAL E 119 " ideal model delta sigma weight residual 113.10 109.53 3.57 9.70e-01 1.06e+00 1.36e+01 angle pdb=" CA SER K 524 " pdb=" C SER K 524 " pdb=" O SER K 524 " ideal model delta sigma weight residual 122.37 118.26 4.11 1.15e+00 7.56e-01 1.28e+01 angle pdb=" N TYR H 37 " pdb=" CA TYR H 37 " pdb=" C TYR H 37 " ideal model delta sigma weight residual 113.21 109.43 3.78 1.15e+00 7.56e-01 1.08e+01 ... (remaining 17111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 5305 35.25 - 70.50: 1265 70.50 - 105.75: 23 105.75 - 141.01: 1 141.01 - 176.26: 2 Dihedral angle restraints: 6596 sinusoidal: 4351 harmonic: 2245 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA HIS F 75 " pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG E 133 " pdb=" C ARG E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1668 0.063 - 0.126: 252 0.126 - 0.189: 24 0.189 - 0.252: 3 0.252 - 0.315: 1 Chirality restraints: 1948 Sorted by residual: chirality pdb=" CA TYR E 110 " pdb=" N TYR E 110 " pdb=" C TYR E 110 " pdb=" CB TYR E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ARG E 80 " pdb=" N ARG E 80 " pdb=" C ARG E 80 " pdb=" CB ARG E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 1945 not shown) Planarity restraints: 1307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 5 " 0.029 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" N1 DT I 5 " -0.031 2.00e-02 2.50e+03 pdb=" C2 DT I 5 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 5 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 5 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 5 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 5 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 5 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " -0.029 2.00e-02 2.50e+03 1.27e-02 4.45e+00 pdb=" N9 DA I 57 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 118 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C ARG E 118 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG E 118 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 119 " 0.010 2.00e-02 2.50e+03 ... (remaining 1304 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2013 2.76 - 3.30: 10136 3.30 - 3.83: 22576 3.83 - 4.37: 27405 4.37 - 4.90: 37724 Nonbonded interactions: 99854 Sorted by model distance: nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.229 3.040 nonbonded pdb=" O SER C 16 " pdb=" OG SER C 19 " model vdw 2.255 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR L 514 " pdb=" N SER L 515 " model vdw 2.266 3.120 nonbonded pdb=" NH2 ARG E 69 " pdb=" OP2 DA I 17 " model vdw 2.277 3.120 ... (remaining 99849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } 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: 3.250 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.270 Find NCS groups from input model: 0.290 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3661 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 : 0.010 0.054 11895 Z= 0.574 Angle : 0.776 8.174 17116 Z= 0.492 Chirality : 0.047 0.315 1948 Planarity : 0.004 0.038 1307 Dihedral : 28.133 176.257 5146 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.31 % Allowed : 13.53 % Favored : 86.16 % 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: -0.89 (0.27), residues: 759 helix: 0.24 (0.20), residues: 541 sheet: None (None), residues: 0 loop : -2.63 (0.31), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 531 HIS 0.007 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.002 TYR F 51 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.944 Fit side-chains REVERT: A 107 GLU cc_start: 0.4059 (mt-10) cc_final: 0.3831 (mt-10) REVERT: A 137 GLU cc_start: 0.4620 (tt0) cc_final: 0.4236 (tt0) REVERT: B 44 LYS cc_start: 0.5387 (mtmt) cc_final: 0.4830 (tttt) REVERT: B 78 ARG cc_start: 0.5414 (mtm-85) cc_final: 0.5186 (mtm110) REVERT: C 20 ARG cc_start: 0.4966 (ttm110) cc_final: 0.4624 (mtm180) REVERT: D 71 GLU cc_start: 0.4649 (tm-30) cc_final: 0.4446 (tp30) REVERT: E 57 SER cc_start: 0.5724 (t) cc_final: 0.5509 (p) REVERT: E 82 VAL cc_start: 0.4383 (OUTLIER) cc_final: 0.4164 (p) REVERT: E 83 ASP cc_start: 0.6312 (p0) cc_final: 0.6030 (t70) REVERT: F 31 LYS cc_start: 0.5009 (mttp) cc_final: 0.4705 (mtpt) REVERT: F 44 LYS cc_start: 0.5327 (tttt) cc_final: 0.4232 (mttt) REVERT: F 63 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5168 (mt-10) REVERT: F 91 LYS cc_start: 0.5476 (tttm) cc_final: 0.5205 (ttpp) REVERT: G 36 LYS cc_start: 0.5899 (mptt) cc_final: 0.5657 (pttt) REVERT: G 104 GLN cc_start: 0.5425 (mm-40) cc_final: 0.5119 (mm110) REVERT: L 525 ARG cc_start: 0.5300 (mtm-85) cc_final: 0.5074 (mtt-85) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 2.0843 time to fit residues: 377.6833 Evaluate side-chains 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN C 94 ASN C 104 GLN D 47 GLN D 84 ASN E 87 GLN E 115 HIS F 27 GLN F 75 HIS F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3616 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11895 Z= 0.216 Angle : 0.625 7.567 17116 Z= 0.370 Chirality : 0.036 0.133 1948 Planarity : 0.004 0.039 1307 Dihedral : 30.918 177.513 3648 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.95 % Allowed : 18.66 % Favored : 78.38 % 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: 1.05 (0.28), residues: 759 helix: 1.61 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.010 0.002 TYR B 51 ARG 0.003 0.000 ARG L 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.940 Fit side-chains REVERT: A 137 GLU cc_start: 0.4398 (tt0) cc_final: 0.4194 (tt0) REVERT: B 44 LYS cc_start: 0.5178 (mttt) cc_final: 0.4723 (tttt) REVERT: B 78 ARG cc_start: 0.5554 (mtm-85) cc_final: 0.5172 (mtm110) REVERT: E 57 SER cc_start: 0.5523 (t) cc_final: 0.5302 (p) REVERT: E 83 ASP cc_start: 0.6569 (p0) cc_final: 0.6249 (t0) REVERT: F 31 LYS cc_start: 0.4583 (mttp) cc_final: 0.4324 (mtpt) REVERT: F 44 LYS cc_start: 0.5320 (tttt) cc_final: 0.4280 (mttt) REVERT: F 63 GLU cc_start: 0.5177 (mt-10) cc_final: 0.4941 (mt-10) REVERT: G 36 LYS cc_start: 0.6000 (mptt) cc_final: 0.5711 (pttt) REVERT: G 104 GLN cc_start: 0.5359 (mm-40) cc_final: 0.5154 (mm110) REVERT: H 47 GLN cc_start: 0.6255 (mt0) cc_final: 0.5954 (mt0) REVERT: H 51 ASP cc_start: 0.6134 (p0) cc_final: 0.5777 (m-30) REVERT: H 57 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.5155 (mtpt) outliers start: 19 outliers final: 5 residues processed: 138 average time/residue: 2.0038 time to fit residues: 290.4721 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.0370 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3628 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11895 Z= 0.324 Angle : 0.677 8.483 17116 Z= 0.395 Chirality : 0.040 0.145 1948 Planarity : 0.005 0.054 1307 Dihedral : 31.216 175.257 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 18.82 % Favored : 77.60 % 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: 1.25 (0.28), residues: 759 helix: 1.65 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 531 HIS 0.005 0.002 HIS B 75 PHE 0.016 0.003 PHE A 78 TYR 0.013 0.002 TYR E 110 ARG 0.007 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.905 Fit side-chains REVERT: A 133 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4392 (mtp85) REVERT: A 137 GLU cc_start: 0.4299 (tt0) cc_final: 0.4020 (tt0) REVERT: B 44 LYS cc_start: 0.5355 (mttt) cc_final: 0.4899 (tttt) REVERT: B 78 ARG cc_start: 0.5427 (mtm-85) cc_final: 0.4972 (mtm110) REVERT: C 77 ARG cc_start: 0.2470 (OUTLIER) cc_final: 0.1726 (ttt-90) REVERT: E 49 LYS cc_start: 0.5318 (tttp) cc_final: 0.5066 (tmtp) REVERT: E 57 SER cc_start: 0.5247 (t) cc_final: 0.4908 (p) REVERT: E 82 VAL cc_start: 0.4755 (OUTLIER) cc_final: 0.4531 (p) REVERT: E 83 ASP cc_start: 0.6666 (p0) cc_final: 0.6394 (t70) REVERT: F 31 LYS cc_start: 0.4508 (mttp) cc_final: 0.4248 (mtpt) REVERT: F 44 LYS cc_start: 0.5439 (tttt) cc_final: 0.4322 (mtmt) REVERT: F 63 GLU cc_start: 0.5113 (mt-10) cc_final: 0.4890 (mt-10) REVERT: F 93 GLN cc_start: 0.4548 (mt0) cc_final: 0.4342 (mt0) REVERT: G 36 LYS cc_start: 0.5985 (mptt) cc_final: 0.5759 (pttt) REVERT: G 104 GLN cc_start: 0.5287 (mm-40) cc_final: 0.5059 (mm110) REVERT: H 47 GLN cc_start: 0.6219 (mt0) cc_final: 0.5952 (mt0) REVERT: H 51 ASP cc_start: 0.6048 (p0) cc_final: 0.5765 (m-30) REVERT: K 525 ARG cc_start: 0.4173 (mtm-85) cc_final: 0.3952 (mpt180) outliers start: 23 outliers final: 5 residues processed: 131 average time/residue: 2.0872 time to fit residues: 286.7074 Evaluate side-chains 124 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN F 64 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3630 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11895 Z= 0.330 Angle : 0.683 8.393 17116 Z= 0.397 Chirality : 0.040 0.152 1948 Planarity : 0.005 0.062 1307 Dihedral : 31.133 171.995 3647 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.73 % Allowed : 18.82 % Favored : 77.45 % 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: 1.30 (0.28), residues: 759 helix: 1.65 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -1.18 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 531 HIS 0.006 0.002 HIS B 75 PHE 0.016 0.003 PHE A 78 TYR 0.014 0.002 TYR B 51 ARG 0.005 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.896 Fit side-chains REVERT: A 133 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4439 (mtp85) REVERT: B 44 LYS cc_start: 0.5269 (mttt) cc_final: 0.4832 (tttt) REVERT: B 78 ARG cc_start: 0.5469 (mtm-85) cc_final: 0.5042 (mtm110) REVERT: C 77 ARG cc_start: 0.2494 (OUTLIER) cc_final: 0.1853 (ttt-90) REVERT: C 111 ILE cc_start: 0.3019 (pt) cc_final: 0.2635 (pp) REVERT: E 49 LYS cc_start: 0.5329 (tttp) cc_final: 0.5066 (tmtp) REVERT: E 82 VAL cc_start: 0.4809 (OUTLIER) cc_final: 0.4594 (p) REVERT: E 83 ASP cc_start: 0.6710 (p0) cc_final: 0.6461 (t70) REVERT: F 31 LYS cc_start: 0.4520 (mttp) cc_final: 0.4259 (mtpt) REVERT: F 44 LYS cc_start: 0.5483 (tttt) cc_final: 0.4379 (mtmt) REVERT: F 63 GLU cc_start: 0.5100 (mt-10) cc_final: 0.4895 (mt-10) REVERT: G 36 LYS cc_start: 0.5914 (mptt) cc_final: 0.5701 (pttt) REVERT: G 104 GLN cc_start: 0.5302 (mm-40) cc_final: 0.5099 (mm110) REVERT: H 47 GLN cc_start: 0.6227 (mt0) cc_final: 0.5970 (mt0) REVERT: H 51 ASP cc_start: 0.6051 (p0) cc_final: 0.5811 (m-30) REVERT: K 526 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.4865 (mpt-90) outliers start: 24 outliers final: 8 residues processed: 135 average time/residue: 2.0115 time to fit residues: 285.3816 Evaluate side-chains 132 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3625 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 0.041 11895 Z= 0.248 Angle : 0.645 8.149 17116 Z= 0.380 Chirality : 0.038 0.139 1948 Planarity : 0.005 0.053 1307 Dihedral : 31.117 171.384 3647 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 19.91 % Favored : 76.52 % 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: 1.57 (0.28), residues: 759 helix: 1.83 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 531 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.060 Fit side-chains REVERT: A 133 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4403 (mtp85) REVERT: B 44 LYS cc_start: 0.5240 (mttt) cc_final: 0.4819 (tttt) REVERT: B 78 ARG cc_start: 0.5501 (mtm-85) cc_final: 0.5081 (mtm110) REVERT: C 38 ASN cc_start: 0.4520 (p0) cc_final: 0.4178 (p0) REVERT: C 77 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.1857 (ttt-90) REVERT: C 111 ILE cc_start: 0.3095 (pt) cc_final: 0.2727 (pp) REVERT: E 49 LYS cc_start: 0.5308 (tttp) cc_final: 0.5043 (tmtp) REVERT: E 82 VAL cc_start: 0.4808 (OUTLIER) cc_final: 0.4590 (p) REVERT: E 83 ASP cc_start: 0.6771 (p0) cc_final: 0.6535 (t70) REVERT: F 31 LYS cc_start: 0.4635 (mttp) cc_final: 0.4360 (mtpt) REVERT: F 44 LYS cc_start: 0.5470 (tttt) cc_final: 0.4356 (mttt) REVERT: G 36 LYS cc_start: 0.5933 (mptt) cc_final: 0.5713 (pttt) REVERT: H 47 GLN cc_start: 0.6202 (mt0) cc_final: 0.5968 (mt0) REVERT: H 51 ASP cc_start: 0.6033 (p0) cc_final: 0.5809 (m-30) REVERT: H 57 LYS cc_start: 0.5374 (OUTLIER) cc_final: 0.5015 (mtpt) REVERT: K 526 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4805 (mpt-90) outliers start: 23 outliers final: 10 residues processed: 133 average time/residue: 1.9668 time to fit residues: 274.8385 Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN F 64 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3620 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11895 Z= 0.209 Angle : 0.628 8.132 17116 Z= 0.371 Chirality : 0.037 0.161 1948 Planarity : 0.005 0.071 1307 Dihedral : 31.072 171.921 3647 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 19.91 % Favored : 76.52 % 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: 1.81 (0.29), residues: 759 helix: 2.01 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.012 0.002 TYR B 51 ARG 0.010 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.960 Fit side-chains REVERT: A 133 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4405 (mtp85) REVERT: B 44 LYS cc_start: 0.5293 (mttt) cc_final: 0.4855 (tttt) REVERT: B 78 ARG cc_start: 0.5469 (mtm-85) cc_final: 0.5060 (mtm110) REVERT: C 38 ASN cc_start: 0.4493 (p0) cc_final: 0.4151 (p0) REVERT: C 77 ARG cc_start: 0.2439 (OUTLIER) cc_final: 0.1763 (ttt-90) REVERT: C 111 ILE cc_start: 0.3150 (pt) cc_final: 0.2797 (pp) REVERT: E 82 VAL cc_start: 0.4782 (OUTLIER) cc_final: 0.4571 (p) REVERT: E 83 ASP cc_start: 0.6815 (p0) cc_final: 0.6602 (t70) REVERT: F 31 LYS cc_start: 0.4615 (mttp) cc_final: 0.4344 (mtpt) REVERT: F 44 LYS cc_start: 0.5464 (tttt) cc_final: 0.4354 (mttt) REVERT: G 36 LYS cc_start: 0.6011 (mptt) cc_final: 0.5788 (pttt) REVERT: H 47 GLN cc_start: 0.6210 (mt0) cc_final: 0.5967 (mt0) REVERT: H 51 ASP cc_start: 0.5960 (p0) cc_final: 0.5739 (m-30) REVERT: H 57 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5135 (mtpt) REVERT: K 526 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.4789 (mpt-90) outliers start: 23 outliers final: 10 residues processed: 137 average time/residue: 2.0124 time to fit residues: 290.0685 Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN F 64 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3628 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11895 Z= 0.273 Angle : 0.647 7.994 17116 Z= 0.379 Chirality : 0.038 0.136 1948 Planarity : 0.005 0.060 1307 Dihedral : 31.063 175.851 3647 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.73 % Allowed : 19.60 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 759 helix: 1.96 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 531 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.014 0.002 TYR B 51 ARG 0.007 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.890 Fit side-chains REVERT: A 133 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.4420 (mtp85) REVERT: B 44 LYS cc_start: 0.5221 (mttt) cc_final: 0.4793 (tttt) REVERT: B 78 ARG cc_start: 0.5462 (mtm-85) cc_final: 0.5028 (mtm110) REVERT: C 77 ARG cc_start: 0.2403 (OUTLIER) cc_final: 0.1775 (ttt-90) REVERT: C 92 GLU cc_start: 0.4796 (mt-10) cc_final: 0.4594 (mt-10) REVERT: C 111 ILE cc_start: 0.3162 (pt) cc_final: 0.2866 (pp) REVERT: D 71 GLU cc_start: 0.4384 (tm-30) cc_final: 0.4173 (tp30) REVERT: F 23 ARG cc_start: 0.3134 (OUTLIER) cc_final: 0.2485 (tmm-80) REVERT: F 31 LYS cc_start: 0.4608 (mttp) cc_final: 0.4341 (mtpt) REVERT: F 44 LYS cc_start: 0.5495 (tttt) cc_final: 0.4359 (mttt) REVERT: G 36 LYS cc_start: 0.6006 (mptt) cc_final: 0.5789 (pttt) REVERT: H 47 GLN cc_start: 0.6241 (mt0) cc_final: 0.5993 (mt0) REVERT: K 526 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4776 (mpt-90) outliers start: 24 outliers final: 11 residues processed: 139 average time/residue: 1.9965 time to fit residues: 291.5211 Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3625 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11895 Z= 0.274 Angle : 0.643 7.870 17116 Z= 0.377 Chirality : 0.038 0.140 1948 Planarity : 0.005 0.043 1307 Dihedral : 31.049 179.468 3647 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.42 % Allowed : 20.22 % Favored : 76.36 % 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: 1.77 (0.29), residues: 759 helix: 1.95 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 531 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.002 TYR D 42 ARG 0.006 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.880 Fit side-chains REVERT: A 133 ARG cc_start: 0.5027 (OUTLIER) cc_final: 0.4434 (mtp85) REVERT: B 44 LYS cc_start: 0.5210 (mttt) cc_final: 0.4784 (tttt) REVERT: B 78 ARG cc_start: 0.5473 (mtm-85) cc_final: 0.5055 (mtm110) REVERT: C 38 ASN cc_start: 0.4558 (p0) cc_final: 0.4232 (p0) REVERT: C 111 ILE cc_start: 0.3089 (pt) cc_final: 0.2809 (pp) REVERT: F 23 ARG cc_start: 0.3057 (OUTLIER) cc_final: 0.2407 (tmm-80) REVERT: F 31 LYS cc_start: 0.4606 (mttp) cc_final: 0.4339 (mtpt) REVERT: F 44 LYS cc_start: 0.5511 (tttt) cc_final: 0.4378 (mttt) REVERT: G 36 LYS cc_start: 0.6014 (mptt) cc_final: 0.5798 (pttt) REVERT: H 47 GLN cc_start: 0.6228 (mt0) cc_final: 0.5981 (mt0) REVERT: K 526 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.4785 (mpt-90) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 2.0168 time to fit residues: 290.0238 Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3642 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11895 Z= 0.468 Angle : 0.761 8.832 17116 Z= 0.435 Chirality : 0.045 0.175 1948 Planarity : 0.006 0.053 1307 Dihedral : 31.570 176.840 3647 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.89 % Allowed : 20.53 % Favored : 75.58 % 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: 1.20 (0.28), residues: 759 helix: 1.53 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP L 530 HIS 0.006 0.002 HIS D 49 PHE 0.019 0.004 PHE A 78 TYR 0.015 0.003 TYR B 51 ARG 0.007 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.774 Fit side-chains REVERT: A 133 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.4484 (mtp85) REVERT: B 44 LYS cc_start: 0.5392 (mttt) cc_final: 0.4805 (tttt) REVERT: B 78 ARG cc_start: 0.5364 (mtm-85) cc_final: 0.4896 (mtm110) REVERT: B 92 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.4469 (ptm160) REVERT: C 111 ILE cc_start: 0.3262 (pt) cc_final: 0.2987 (pp) REVERT: F 31 LYS cc_start: 0.4573 (mttp) cc_final: 0.4306 (mtpt) REVERT: F 44 LYS cc_start: 0.5521 (tttt) cc_final: 0.4333 (mtmt) REVERT: H 47 GLN cc_start: 0.6192 (mt0) cc_final: 0.5961 (mt0) REVERT: H 68 ASP cc_start: 0.5208 (t70) cc_final: 0.5000 (t0) REVERT: K 526 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4779 (mpt-90) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 1.9912 time to fit residues: 284.6018 Evaluate side-chains 131 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3623 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11895 Z= 0.228 Angle : 0.661 8.179 17116 Z= 0.388 Chirality : 0.038 0.144 1948 Planarity : 0.004 0.042 1307 Dihedral : 31.415 177.191 3647 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.02 % Allowed : 22.71 % Favored : 75.27 % 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: 1.63 (0.29), residues: 759 helix: 1.84 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 530 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.002 PHE E 67 TYR 0.012 0.002 TYR B 51 ARG 0.011 0.001 ARG F 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.843 Fit side-chains REVERT: B 44 LYS cc_start: 0.5230 (mttt) cc_final: 0.4825 (tttt) REVERT: B 78 ARG cc_start: 0.5488 (mtm-85) cc_final: 0.5035 (mtm110) REVERT: B 92 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4779 (ptm-80) REVERT: C 38 ASN cc_start: 0.4298 (p0) cc_final: 0.4034 (p0) REVERT: C 111 ILE cc_start: 0.3257 (pt) cc_final: 0.3011 (pp) REVERT: F 31 LYS cc_start: 0.4692 (mttp) cc_final: 0.4397 (mtpt) REVERT: F 44 LYS cc_start: 0.5407 (tttt) cc_final: 0.4250 (mttt) REVERT: H 47 GLN cc_start: 0.6164 (mt0) cc_final: 0.5941 (mt0) REVERT: K 526 ARG cc_start: 0.5380 (OUTLIER) cc_final: 0.4744 (mpt-90) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 2.0499 time to fit residues: 286.0879 Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 526 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115685 restraints weight = 12942.858| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 0.97 r_work: 0.3100 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11895 Z= 0.242 Angle : 0.634 7.625 17116 Z= 0.373 Chirality : 0.037 0.138 1948 Planarity : 0.004 0.048 1307 Dihedral : 31.003 177.597 3647 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.33 % Allowed : 22.71 % Favored : 74.96 % 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: 1.84 (0.29), residues: 759 helix: 2.00 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 530 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.008 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.23 seconds wall clock time: 85 minutes 25.38 seconds (5125.38 seconds total)