Starting phenix.real_space_refine on Tue Jul 29 17:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.map" model { file = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2025/7ohc_12900.cif" } resolution = 2.5 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= 0.003 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 289 5.49 5 S 12 5.16 5 C 6648 2.51 5 N 2262 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" 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: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 7.17, per 1000 atoms: 0.60 Number of scatterers: 12019 At special positions: 0 Unit cell: (74.55, 119.7, 115.5, 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 12 16.00 P 289 15.00 O 2808 8.00 N 2262 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 900.2 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.3% alpha, 3.1% beta 144 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.244A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 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: 4.340A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.030A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.355A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.461A 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 42 through 43 removed outlier: 7.407A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 3.40 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: 1813 1.33 - 1.45: 4503 1.45 - 1.57: 5904 1.57 - 1.69: 580 1.69 - 1.81: 22 Bond restraints: 12822 Sorted by residual: bond pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.41e+01 bond pdb=" CG GLU H 110 " pdb=" CD GLU H 110 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.24e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.57e+00 bond pdb=" CD GLU H 110 " pdb=" OE2 GLU H 110 " ideal model delta sigma weight residual 1.249 1.209 0.040 1.90e-02 2.77e+03 4.39e+00 ... (remaining 12817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17923 2.09 - 4.17: 563 4.17 - 6.26: 40 6.26 - 8.34: 19 8.34 - 10.43: 11 Bond angle restraints: 18556 Sorted by residual: angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.03e+01 angle pdb=" C ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 119.26 -8.70 1.69e+00 3.50e-01 2.65e+01 angle pdb=" CA THR A 58 " pdb=" CB THR A 58 " pdb=" CG2 THR A 58 " ideal model delta sigma weight residual 110.50 118.23 -7.73 1.70e+00 3.46e-01 2.07e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 104.19 6.37 1.46e+00 4.69e-01 1.90e+01 angle pdb=" CA LYS G 74 " pdb=" CB LYS G 74 " pdb=" CG LYS G 74 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 ... (remaining 18551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4465 21.47 - 42.93: 1384 42.93 - 64.40: 1085 64.40 - 85.87: 47 85.87 - 107.34: 4 Dihedral angle restraints: 6985 sinusoidal: 4767 harmonic: 2218 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1910 0.082 - 0.165: 191 0.165 - 0.247: 9 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CB THR D 116 " pdb=" CA THR D 116 " pdb=" OG1 THR D 116 " pdb=" CG2 THR D 116 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2108 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN C 73 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR A 58 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.036 2.00e-02 2.50e+03 2.11e-02 9.97e+00 pdb=" N1 DC I 69 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.010 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 951 2.73 - 3.28: 10386 3.28 - 3.82: 24870 3.82 - 4.36: 30273 4.36 - 4.90: 41885 Nonbonded interactions: 108365 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.238 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.255 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.275 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.299 3.040 ... (remaining 108360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) selection = chain 'H' } 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=0.00 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: 0.460 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 0.113 12822 Z= 0.235 Angle : 0.856 10.429 18556 Z= 0.503 Chirality : 0.049 0.412 2111 Planarity : 0.006 0.052 1344 Dihedral : 29.622 107.336 5553 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.16 % Allowed : 15.70 % Favored : 84.14 % 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: 0.04 (0.27), residues: 748 helix: 0.44 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.029 0.003 PHE G 25 TYR 0.051 0.003 TYR H 118 ARG 0.014 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.10696 ( 786) hydrogen bonds : angle 4.11912 ( 1972) covalent geometry : bond 0.00531 (12822) covalent geometry : angle 0.85629 (18556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.866 Fit side-chains REVERT: A 42 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7580 (mmm-85) REVERT: A 50 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 90 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t0) REVERT: D 31 LYS cc_start: 0.8728 (mptt) cc_final: 0.8420 (mmtm) REVERT: D 68 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tp30) REVERT: D 90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7932 (mp0) REVERT: D 105 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8266 (ttpp) REVERT: E 129 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8010 (tpt90) REVERT: G 74 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8400 (mtmm) REVERT: G 99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7691 (mmm-85) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8469 (t0) REVERT: H 76 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7532 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 1.7265 time to fit residues: 374.1903 Evaluate side-chains 184 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081045 restraints weight = 20144.983| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.38 r_work: 0.3080 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12822 Z= 0.263 Angle : 0.622 5.737 18556 Z= 0.373 Chirality : 0.038 0.170 2111 Planarity : 0.005 0.046 1344 Dihedral : 31.626 106.575 4030 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.83 % Allowed : 17.27 % Favored : 79.91 % 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: 1.58 (0.29), residues: 748 helix: 1.61 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.023 0.002 PHE G 25 TYR 0.017 0.002 TYR H 37 ARG 0.006 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 786) hydrogen bonds : angle 3.14479 ( 1972) covalent geometry : bond 0.00590 (12822) covalent geometry : angle 0.62193 (18556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.077 Fit side-chains REVERT: A 42 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7433 (mmm-85) REVERT: A 50 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 64 GLU cc_start: 0.8527 (tt0) cc_final: 0.8169 (tp30) REVERT: C 73 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8569 (t0) REVERT: C 90 ASP cc_start: 0.8487 (t70) cc_final: 0.8191 (t70) REVERT: D 68 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8264 (tp30) REVERT: D 90 GLU cc_start: 0.8761 (mp0) cc_final: 0.8458 (mp0) REVERT: E 68 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: E 129 ARG cc_start: 0.8661 (tpt90) cc_final: 0.8177 (tpt90) REVERT: F 63 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: G 113 SER cc_start: 0.8951 (m) cc_final: 0.8730 (p) REVERT: H 39 TYR cc_start: 0.8229 (t80) cc_final: 0.8005 (t80) REVERT: H 65 ASP cc_start: 0.9054 (t70) cc_final: 0.8781 (t0) REVERT: H 76 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8023 (mtm-85) outliers start: 18 outliers final: 4 residues processed: 192 average time/residue: 1.8450 time to fit residues: 374.3010 Evaluate side-chains 186 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082474 restraints weight = 20237.377| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.37 r_work: 0.3105 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12822 Z= 0.170 Angle : 0.582 5.347 18556 Z= 0.355 Chirality : 0.034 0.157 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.593 107.438 4030 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.30 % Allowed : 19.00 % Favored : 77.71 % 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: 2.16 (0.29), residues: 748 helix: 2.05 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.26 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.002 TYR G 57 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 786) hydrogen bonds : angle 3.04384 ( 1972) covalent geometry : bond 0.00370 (12822) covalent geometry : angle 0.58163 (18556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.941 Fit side-chains REVERT: A 42 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7822 (mmm-85) REVERT: A 50 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 64 GLU cc_start: 0.8433 (tt0) cc_final: 0.8058 (tp30) REVERT: C 73 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8458 (t0) REVERT: C 75 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8746 (mmmm) REVERT: C 90 ASP cc_start: 0.8491 (t70) cc_final: 0.8158 (t70) REVERT: D 68 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8191 (tp30) REVERT: D 90 GLU cc_start: 0.8746 (mp0) cc_final: 0.8490 (mp0) REVERT: E 68 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: E 129 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8203 (tpt90) REVERT: G 113 SER cc_start: 0.8930 (m) cc_final: 0.8694 (p) REVERT: H 39 TYR cc_start: 0.8182 (t80) cc_final: 0.7865 (t80) REVERT: H 65 ASP cc_start: 0.9023 (t70) cc_final: 0.8759 (t0) REVERT: H 76 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7849 (mtm-85) outliers start: 21 outliers final: 11 residues processed: 188 average time/residue: 1.7435 time to fit residues: 346.7740 Evaluate side-chains 195 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083102 restraints weight = 20060.055| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.35 r_work: 0.3129 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12822 Z= 0.178 Angle : 0.561 7.713 18556 Z= 0.342 Chirality : 0.034 0.173 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.117 108.857 4030 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.45 % Allowed : 19.15 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 748 helix: 2.34 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE G 25 TYR 0.011 0.001 TYR D 37 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 786) hydrogen bonds : angle 2.91925 ( 1972) covalent geometry : bond 0.00390 (12822) covalent geometry : angle 0.56097 (18556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8457 (t0) REVERT: C 75 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8741 (mmmm) REVERT: C 90 ASP cc_start: 0.8373 (t70) cc_final: 0.8058 (t70) REVERT: D 90 GLU cc_start: 0.8720 (mp0) cc_final: 0.8451 (mp0) REVERT: E 68 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: E 129 ARG cc_start: 0.8586 (tpt90) cc_final: 0.8161 (tpt90) REVERT: H 30 ARG cc_start: 0.6547 (mtp-110) cc_final: 0.6245 (mtt180) REVERT: H 39 TYR cc_start: 0.8312 (t80) cc_final: 0.8054 (t80) REVERT: H 76 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7920 (mtm-85) outliers start: 22 outliers final: 8 residues processed: 196 average time/residue: 1.8374 time to fit residues: 380.0360 Evaluate side-chains 195 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN C 24 GLN G 104 GLN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081301 restraints weight = 20090.385| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.37 r_work: 0.3094 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12822 Z= 0.223 Angle : 0.582 6.309 18556 Z= 0.352 Chirality : 0.035 0.182 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.128 113.163 4030 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.30 % Allowed : 20.41 % Favored : 76.30 % 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: 2.56 (0.30), residues: 748 helix: 2.32 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.05 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE G 25 TYR 0.018 0.002 TYR G 57 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 786) hydrogen bonds : angle 2.96759 ( 1972) covalent geometry : bond 0.00498 (12822) covalent geometry : angle 0.58174 (18556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.484 Fit side-chains REVERT: A 42 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (mtp-110) REVERT: C 73 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8397 (t0) REVERT: C 75 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8793 (mmmm) REVERT: C 90 ASP cc_start: 0.8397 (t70) cc_final: 0.8100 (t70) REVERT: C 91 GLU cc_start: 0.8258 (pm20) cc_final: 0.8014 (pm20) REVERT: D 54 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8669 (mmtp) REVERT: E 68 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8785 (tt0) REVERT: E 129 ARG cc_start: 0.8597 (tpt90) cc_final: 0.8135 (tpt90) REVERT: F 93 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: G 74 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8482 (mtmm) REVERT: H 30 ARG cc_start: 0.6789 (mtp-110) cc_final: 0.6473 (mtt180) REVERT: H 39 TYR cc_start: 0.8324 (t80) cc_final: 0.8067 (t80) REVERT: H 76 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7868 (mtm-85) outliers start: 21 outliers final: 8 residues processed: 191 average time/residue: 2.7857 time to fit residues: 564.6701 Evaluate side-chains 198 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081939 restraints weight = 20438.425| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.36 r_work: 0.3119 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12822 Z= 0.189 Angle : 0.581 6.261 18556 Z= 0.351 Chirality : 0.034 0.162 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.119 113.561 4030 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.30 % Allowed : 21.19 % Favored : 75.51 % 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: 2.64 (0.30), residues: 748 helix: 2.38 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.02 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.022 0.002 TYR G 57 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 786) hydrogen bonds : angle 2.97548 ( 1972) covalent geometry : bond 0.00420 (12822) covalent geometry : angle 0.58134 (18556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.865 Fit side-chains REVERT: C 73 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8329 (t0) REVERT: C 75 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8784 (mmmm) REVERT: C 90 ASP cc_start: 0.8395 (t70) cc_final: 0.8072 (t70) REVERT: D 54 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8605 (mmtp) REVERT: E 68 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: E 120 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7875 (mtt) REVERT: E 129 ARG cc_start: 0.8606 (tpt90) cc_final: 0.8146 (tpt90) REVERT: F 93 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: G 64 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: G 74 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: H 30 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6475 (mtt180) REVERT: H 39 TYR cc_start: 0.8271 (t80) cc_final: 0.8007 (t80) REVERT: H 68 GLU cc_start: 0.8397 (pt0) cc_final: 0.8189 (pt0) REVERT: H 76 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7860 (mtm-85) outliers start: 21 outliers final: 9 residues processed: 187 average time/residue: 1.9248 time to fit residues: 379.9025 Evaluate side-chains 197 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.103615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082042 restraints weight = 20376.250| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.35 r_work: 0.3119 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12822 Z= 0.205 Angle : 0.575 6.223 18556 Z= 0.349 Chirality : 0.035 0.150 2111 Planarity : 0.004 0.042 1344 Dihedral : 30.935 117.744 4030 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.98 % Allowed : 21.66 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.30), residues: 748 helix: 2.39 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.018 0.002 TYR F 88 ARG 0.008 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 786) hydrogen bonds : angle 2.94518 ( 1972) covalent geometry : bond 0.00455 (12822) covalent geometry : angle 0.57516 (18556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.862 Fit side-chains REVERT: A 42 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.8061 (mtp85) REVERT: C 64 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8242 (tp30) REVERT: C 73 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8429 (t0) REVERT: C 75 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8771 (mmmm) REVERT: C 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8143 (t70) REVERT: D 54 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8643 (mmtp) REVERT: E 68 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: E 79 LYS cc_start: 0.9124 (tttp) cc_final: 0.8913 (tttm) REVERT: E 129 ARG cc_start: 0.8578 (tpt90) cc_final: 0.8258 (tpt90) REVERT: F 93 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: G 64 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: G 74 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8515 (mtmm) REVERT: G 92 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8318 (mt-10) REVERT: H 30 ARG cc_start: 0.6783 (mtp-110) cc_final: 0.6485 (mtt180) REVERT: H 39 TYR cc_start: 0.8271 (t80) cc_final: 0.8027 (t80) REVERT: H 68 GLU cc_start: 0.8403 (pt0) cc_final: 0.8139 (pt0) REVERT: H 76 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7917 (mtm-85) outliers start: 19 outliers final: 10 residues processed: 185 average time/residue: 1.8260 time to fit residues: 356.3826 Evaluate side-chains 196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.082553 restraints weight = 20493.359| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.36 r_work: 0.3129 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12822 Z= 0.182 Angle : 0.577 9.769 18556 Z= 0.348 Chirality : 0.034 0.142 2111 Planarity : 0.004 0.042 1344 Dihedral : 30.937 118.060 4030 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.98 % Allowed : 22.61 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.30), residues: 748 helix: 2.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.16 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.023 0.002 TYR F 88 ARG 0.009 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 786) hydrogen bonds : angle 2.97436 ( 1972) covalent geometry : bond 0.00403 (12822) covalent geometry : angle 0.57701 (18556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.864 Fit side-chains REVERT: C 64 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8238 (tp30) REVERT: C 73 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8405 (t0) REVERT: C 75 LYS cc_start: 0.9101 (mmtp) cc_final: 0.8761 (mmmm) REVERT: C 90 ASP cc_start: 0.8464 (t70) cc_final: 0.8126 (t70) REVERT: D 54 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8585 (mmtp) REVERT: E 68 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8743 (tt0) REVERT: E 129 ARG cc_start: 0.8576 (tpt90) cc_final: 0.8256 (tpt90) REVERT: F 93 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: G 64 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: G 74 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8514 (mtmm) REVERT: G 92 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8131 (mt-10) REVERT: H 30 ARG cc_start: 0.6790 (mtp-110) cc_final: 0.6496 (mtt180) REVERT: H 39 TYR cc_start: 0.8246 (t80) cc_final: 0.7999 (t80) REVERT: H 68 GLU cc_start: 0.8406 (pt0) cc_final: 0.8171 (pt0) REVERT: H 76 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7895 (mtm-85) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 1.8018 time to fit residues: 348.2128 Evaluate side-chains 195 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082976 restraints weight = 20321.887| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.35 r_work: 0.3139 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12822 Z= 0.166 Angle : 0.577 6.855 18556 Z= 0.348 Chirality : 0.033 0.141 2111 Planarity : 0.004 0.042 1344 Dihedral : 30.939 118.137 4030 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.83 % Allowed : 22.61 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.30), residues: 748 helix: 2.46 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.19 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE A 67 TYR 0.019 0.001 TYR F 88 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 786) hydrogen bonds : angle 2.96223 ( 1972) covalent geometry : bond 0.00364 (12822) covalent geometry : angle 0.57713 (18556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.868 Fit side-chains REVERT: A 42 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7982 (mtp85) REVERT: C 64 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8210 (tp30) REVERT: C 73 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8406 (t0) REVERT: C 75 LYS cc_start: 0.9089 (mmtp) cc_final: 0.8747 (mmmm) REVERT: C 90 ASP cc_start: 0.8451 (t70) cc_final: 0.8132 (t70) REVERT: D 54 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8582 (mmtp) REVERT: E 68 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: E 129 ARG cc_start: 0.8573 (tpt90) cc_final: 0.8254 (tpt90) REVERT: F 93 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: G 64 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: G 74 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8501 (mtmm) REVERT: G 92 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8127 (mt-10) REVERT: H 30 ARG cc_start: 0.6765 (mtp-110) cc_final: 0.6476 (mtt180) REVERT: H 39 TYR cc_start: 0.8236 (t80) cc_final: 0.7989 (t80) REVERT: H 68 GLU cc_start: 0.8365 (pt0) cc_final: 0.8159 (pt0) REVERT: H 76 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (mtm-85) outliers start: 18 outliers final: 10 residues processed: 184 average time/residue: 1.8302 time to fit residues: 356.1752 Evaluate side-chains 196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 99 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN D 44 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083257 restraints weight = 20229.388| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.35 r_work: 0.3144 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12822 Z= 0.163 Angle : 0.575 6.981 18556 Z= 0.348 Chirality : 0.033 0.139 2111 Planarity : 0.004 0.042 1344 Dihedral : 30.928 118.297 4030 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.14 % Allowed : 22.29 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.30), residues: 748 helix: 2.46 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.19 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE A 67 TYR 0.040 0.002 TYR F 88 ARG 0.008 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 786) hydrogen bonds : angle 2.96315 ( 1972) covalent geometry : bond 0.00354 (12822) covalent geometry : angle 0.57504 (18556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.958 Fit side-chains REVERT: A 42 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7974 (mtp85) REVERT: C 64 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8196 (tp30) REVERT: C 73 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8402 (t0) REVERT: C 75 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8748 (mmmm) REVERT: C 90 ASP cc_start: 0.8448 (t70) cc_final: 0.8110 (t70) REVERT: D 54 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8585 (mmtp) REVERT: E 68 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: E 120 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7764 (mtt) REVERT: E 129 ARG cc_start: 0.8573 (tpt90) cc_final: 0.8104 (tpt90) REVERT: F 93 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: G 74 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: G 92 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8125 (mt-10) REVERT: H 30 ARG cc_start: 0.6763 (mtp-110) cc_final: 0.6472 (mtt180) REVERT: H 39 TYR cc_start: 0.8232 (t80) cc_final: 0.7983 (t80) REVERT: H 68 GLU cc_start: 0.8396 (pt0) cc_final: 0.8133 (pt0) REVERT: H 76 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7894 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 182 average time/residue: 1.8034 time to fit residues: 346.6832 Evaluate side-chains 196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.102274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.080387 restraints weight = 20230.798| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.37 r_work: 0.3090 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12822 Z= 0.263 Angle : 0.611 9.404 18556 Z= 0.366 Chirality : 0.037 0.143 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.047 122.296 4030 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.98 % Allowed : 22.29 % Favored : 74.73 % 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: 2.62 (0.30), residues: 748 helix: 2.33 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.16 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE G 25 TYR 0.027 0.002 TYR F 88 ARG 0.010 0.001 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 786) hydrogen bonds : angle 3.04111 ( 1972) covalent geometry : bond 0.00592 (12822) covalent geometry : angle 0.61087 (18556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12276.18 seconds wall clock time: 215 minutes 26.07 seconds (12926.07 seconds total)