Starting phenix.real_space_refine on Sat Apr 6 09:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/04_2024/8fai_28957_updated.pdb" } resolution = 3.0 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 15 5.49 5 S 60 5.16 5 C 5250 2.51 5 N 1140 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7845 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "B" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "D" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "E" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "F" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "G" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "H" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "J" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "L" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "M" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "N" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "O" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.33, per 1000 atoms: 0.55 Number of scatterers: 7845 At special positions: 0 Unit cell: (87.36, 89.024, 93.184, 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 60 16.00 P 15 15.00 O 1380 8.00 N 1140 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 88 Processing helix chain 'C' and resid 94 through 108 Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 70 through 88 Processing helix chain 'D' and resid 94 through 108 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 94 through 108 Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 94 through 108 Processing helix chain 'F' and resid 110 through 117 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 88 Processing helix chain 'G' and resid 94 through 108 Processing helix chain 'G' and resid 110 through 117 Processing helix chain 'H' and resid 56 through 67 Processing helix chain 'H' and resid 70 through 88 Processing helix chain 'H' and resid 94 through 108 Processing helix chain 'H' and resid 110 through 117 Processing helix chain 'I' and resid 56 through 67 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 94 through 108 Processing helix chain 'I' and resid 110 through 117 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 70 through 88 Processing helix chain 'J' and resid 94 through 108 Processing helix chain 'J' and resid 110 through 117 Processing helix chain 'K' and resid 56 through 67 Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'K' and resid 110 through 117 Processing helix chain 'L' and resid 56 through 67 Processing helix chain 'L' and resid 70 through 88 Processing helix chain 'L' and resid 94 through 108 Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'M' and resid 56 through 67 Processing helix chain 'M' and resid 70 through 88 Processing helix chain 'M' and resid 94 through 108 Processing helix chain 'M' and resid 110 through 117 Processing helix chain 'N' and resid 56 through 67 Processing helix chain 'N' and resid 70 through 88 Processing helix chain 'N' and resid 94 through 108 Processing helix chain 'N' and resid 110 through 117 Processing helix chain 'O' and resid 56 through 67 Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 94 through 108 Processing helix chain 'O' and resid 110 through 117 570 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1125 1.31 - 1.43: 1909 1.43 - 1.56: 4631 1.56 - 1.68: 180 1.68 - 1.81: 105 Bond restraints: 7950 Sorted by residual: bond pdb=" O13 XL0 F 200 " pdb=" P XL0 F 200 " ideal model delta sigma weight residual 1.524 1.465 0.059 2.00e-02 2.50e+03 8.66e+00 bond pdb=" O13 XL0 I 200 " pdb=" P XL0 I 200 " ideal model delta sigma weight residual 1.524 1.466 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" O13 XL0 G 200 " pdb=" P XL0 G 200 " ideal model delta sigma weight residual 1.524 1.466 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 XL0 L 201 " pdb=" P XL0 L 201 " ideal model delta sigma weight residual 1.524 1.466 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 XL0 J 200 " pdb=" P XL0 J 200 " ideal model delta sigma weight residual 1.524 1.466 0.058 2.00e-02 2.50e+03 8.49e+00 ... (remaining 7945 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.68: 194 106.68 - 113.48: 4692 113.48 - 120.29: 2589 120.29 - 127.10: 3040 127.10 - 133.91: 75 Bond angle restraints: 10590 Sorted by residual: angle pdb=" C39 XL0 H 200 " pdb="C310 XL0 H 200 " pdb="C311 XL0 H 200 " ideal model delta sigma weight residual 152.61 120.83 31.78 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C39 XL0 F 200 " pdb="C310 XL0 F 200 " pdb="C311 XL0 F 200 " ideal model delta sigma weight residual 152.61 120.86 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C39 XL0 I 200 " pdb="C310 XL0 I 200 " pdb="C311 XL0 I 200 " ideal model delta sigma weight residual 152.61 120.86 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C39 XL0 L 201 " pdb="C310 XL0 L 201 " pdb="C311 XL0 L 201 " ideal model delta sigma weight residual 152.61 121.06 31.55 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C39 XL0 N 201 " pdb="C310 XL0 N 201 " pdb="C311 XL0 N 201 " ideal model delta sigma weight residual 152.61 121.08 31.53 3.00e+00 1.11e-01 1.10e+02 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 4170 34.64 - 69.28: 225 69.28 - 103.92: 45 103.92 - 138.56: 15 138.56 - 173.20: 45 Dihedral angle restraints: 4500 sinusoidal: 1875 harmonic: 2625 Sorted by residual: dihedral pdb=" C23 XL0 L 202 " pdb=" C21 XL0 L 202 " pdb=" C22 XL0 L 202 " pdb=" O21 XL0 L 202 " ideal model delta sinusoidal sigma weight residual 260.94 87.74 173.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 XL0 N 201 " pdb=" C21 XL0 N 201 " pdb=" C22 XL0 N 201 " pdb=" O21 XL0 N 201 " ideal model delta sinusoidal sigma weight residual 260.94 87.75 173.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 XL0 K 201 " pdb=" C21 XL0 K 201 " pdb=" C22 XL0 K 201 " pdb=" O21 XL0 K 201 " ideal model delta sinusoidal sigma weight residual 260.94 87.76 173.18 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 489 0.017 - 0.034: 359 0.034 - 0.051: 156 0.051 - 0.068: 175 0.068 - 0.085: 51 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA PRO G 70 " pdb=" N PRO G 70 " pdb=" C PRO G 70 " pdb=" CB PRO G 70 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.08 2.00e-01 2.50e+01 1.80e-01 chirality pdb=" CA PRO C 70 " pdb=" N PRO C 70 " pdb=" C PRO C 70 " pdb=" CB PRO C 70 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PRO E 70 " pdb=" N PRO E 70 " pdb=" C PRO E 70 " pdb=" CB PRO E 70 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.08 2.00e-01 2.50e+01 1.76e-01 ... (remaining 1227 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 XL0 L 202 " -0.012 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C39 XL0 L 202 " 0.027 2.00e-02 2.50e+03 pdb="C310 XL0 L 202 " -0.027 2.00e-02 2.50e+03 pdb="C311 XL0 L 202 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 XL0 N 201 " 0.012 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C39 XL0 N 201 " -0.027 2.00e-02 2.50e+03 pdb="C310 XL0 N 201 " 0.027 2.00e-02 2.50e+03 pdb="C311 XL0 N 201 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 XL0 G 200 " -0.012 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C39 XL0 G 200 " 0.027 2.00e-02 2.50e+03 pdb="C310 XL0 G 200 " -0.027 2.00e-02 2.50e+03 pdb="C311 XL0 G 200 " 0.012 2.00e-02 2.50e+03 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2845 2.90 - 3.40: 8120 3.40 - 3.90: 13571 3.90 - 4.40: 15198 4.40 - 4.90: 23836 Nonbonded interactions: 63570 Sorted by model distance: nonbonded pdb=" O LEU B 117 " pdb=" OG1 THR B 118 " model vdw 2.395 2.440 nonbonded pdb=" O LEU N 117 " pdb=" OG1 THR N 118 " model vdw 2.395 2.440 nonbonded pdb=" O LEU G 117 " pdb=" OG1 THR G 118 " model vdw 2.396 2.440 nonbonded pdb=" O LEU A 117 " pdb=" OG1 THR A 118 " model vdw 2.396 2.440 nonbonded pdb=" O LEU K 117 " pdb=" OG1 THR K 118 " model vdw 2.396 2.440 ... (remaining 63565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 51 through 118) selection = (chain 'G' and resid 51 through 118) selection = (chain 'H' and resid 51 through 118) selection = (chain 'I' and resid 51 through 118) selection = (chain 'J' and resid 51 through 118) selection = (chain 'K' and resid 51 through 118) selection = (chain 'L' and resid 51 through 118) selection = (chain 'M' and resid 51 through 118) selection = (chain 'N' and resid 51 through 118) selection = (chain 'O' and resid 51 through 118) } 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: 1.180 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: 5.650 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.007 0.059 7950 Z= 0.430 Angle : 1.384 31.780 10590 Z= 0.515 Chirality : 0.035 0.085 1230 Planarity : 0.004 0.022 1260 Dihedral : 29.181 173.199 2880 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.16 (0.27), residues: 990 helix: 2.50 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 87 PHE 0.007 0.001 PHE D 71 ARG 0.001 0.000 ARG O 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 0.740 Fit side-chains REVERT: A 74 SER cc_start: 0.8716 (m) cc_final: 0.8398 (p) REVERT: B 74 SER cc_start: 0.8818 (m) cc_final: 0.8539 (p) REVERT: B 94 LEU cc_start: 0.8697 (tp) cc_final: 0.8410 (tp) REVERT: C 74 SER cc_start: 0.8697 (m) cc_final: 0.8425 (p) REVERT: D 74 SER cc_start: 0.8707 (m) cc_final: 0.8443 (p) REVERT: E 74 SER cc_start: 0.8792 (m) cc_final: 0.8483 (p) REVERT: F 74 SER cc_start: 0.8656 (m) cc_final: 0.8425 (p) REVERT: H 74 SER cc_start: 0.8705 (m) cc_final: 0.8496 (p) outliers start: 0 outliers final: 1 residues processed: 271 average time/residue: 0.7317 time to fit residues: 216.0168 Evaluate side-chains 189 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 107 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 81 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7950 Z= 0.191 Angle : 0.565 6.823 10590 Z= 0.281 Chirality : 0.036 0.185 1230 Planarity : 0.005 0.050 1260 Dihedral : 34.856 179.437 1548 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 6.53 % Allowed : 19.58 % Favored : 73.89 % 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: 3.71 (0.26), residues: 990 helix: 2.72 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -0.64 (0.52), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 87 PHE 0.010 0.001 PHE L 112 ARG 0.014 0.004 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 0.834 Fit side-chains REVERT: A 54 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 91 ARG cc_start: 0.5942 (ppt170) cc_final: 0.5734 (ppt170) REVERT: B 59 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7201 (mtp) REVERT: B 74 SER cc_start: 0.8697 (m) cc_final: 0.8154 (p) REVERT: D 74 SER cc_start: 0.8845 (m) cc_final: 0.8387 (p) REVERT: F 54 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7688 (t) REVERT: F 74 SER cc_start: 0.8650 (m) cc_final: 0.8362 (p) REVERT: G 54 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7658 (t) REVERT: H 54 THR cc_start: 0.7953 (p) cc_final: 0.7544 (t) REVERT: J 54 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7681 (t) REVERT: L 60 VAL cc_start: 0.8543 (t) cc_final: 0.8313 (m) REVERT: L 64 CYS cc_start: 0.7860 (m) cc_final: 0.7658 (m) REVERT: M 60 VAL cc_start: 0.8594 (t) cc_final: 0.8188 (m) REVERT: N 60 VAL cc_start: 0.8358 (t) cc_final: 0.7585 (m) outliers start: 47 outliers final: 32 residues processed: 222 average time/residue: 0.6374 time to fit residues: 156.8415 Evaluate side-chains 215 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 61 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7950 Z= 0.218 Angle : 0.558 8.351 10590 Z= 0.272 Chirality : 0.035 0.217 1230 Planarity : 0.003 0.030 1260 Dihedral : 32.321 178.188 1545 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.78 % Allowed : 23.33 % Favored : 68.89 % 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: 3.59 (0.25), residues: 990 helix: 2.65 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 87 PHE 0.016 0.001 PHE M 112 ARG 0.006 0.002 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 178 time to evaluate : 0.806 Fit side-chains REVERT: A 54 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7844 (t) REVERT: D 65 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8077 (p) REVERT: E 59 MET cc_start: 0.7680 (mtt) cc_final: 0.7376 (mtp) REVERT: E 115 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7408 (mttp) REVERT: F 54 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7964 (t) REVERT: G 54 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7830 (t) REVERT: H 54 THR cc_start: 0.8145 (p) cc_final: 0.7726 (t) REVERT: K 54 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7788 (t) REVERT: L 54 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7873 (t) REVERT: L 60 VAL cc_start: 0.8535 (t) cc_final: 0.8276 (m) REVERT: L 112 PHE cc_start: 0.7497 (m-80) cc_final: 0.7073 (m-10) REVERT: M 54 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7807 (t) REVERT: N 54 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (t) REVERT: N 60 VAL cc_start: 0.8435 (t) cc_final: 0.8085 (m) REVERT: N 93 SER cc_start: 0.8203 (t) cc_final: 0.7866 (p) REVERT: O 54 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7876 (t) outliers start: 56 outliers final: 34 residues processed: 205 average time/residue: 0.6518 time to fit residues: 147.7349 Evaluate side-chains 210 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN M 62 ASN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7950 Z= 0.210 Angle : 0.531 7.920 10590 Z= 0.261 Chirality : 0.035 0.103 1230 Planarity : 0.003 0.024 1260 Dihedral : 31.175 178.034 1545 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 8.19 % Allowed : 26.25 % Favored : 65.56 % 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: 3.52 (0.25), residues: 990 helix: 2.63 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 87 PHE 0.011 0.001 PHE L 112 ARG 0.006 0.002 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 0.851 Fit side-chains REVERT: A 54 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7904 (m) REVERT: A 59 MET cc_start: 0.7633 (mtp) cc_final: 0.7431 (mtp) REVERT: C 54 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.7997 (t) REVERT: D 65 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 59 MET cc_start: 0.7660 (mtt) cc_final: 0.7366 (mtp) REVERT: E 94 LEU cc_start: 0.8834 (tp) cc_final: 0.8608 (tp) REVERT: E 115 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7363 (mttp) REVERT: G 54 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (m) REVERT: J 54 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7982 (m) REVERT: K 54 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7918 (t) REVERT: K 59 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7567 (mtt) REVERT: L 54 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7813 (t) REVERT: M 54 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7698 (t) REVERT: N 54 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7804 (t) REVERT: N 60 VAL cc_start: 0.8394 (t) cc_final: 0.7841 (m) REVERT: N 93 SER cc_start: 0.8187 (t) cc_final: 0.7839 (p) REVERT: O 54 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7911 (t) outliers start: 59 outliers final: 34 residues processed: 206 average time/residue: 0.6054 time to fit residues: 138.4039 Evaluate side-chains 210 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 165 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7950 Z= 0.230 Angle : 0.554 8.667 10590 Z= 0.268 Chirality : 0.035 0.101 1230 Planarity : 0.003 0.025 1260 Dihedral : 30.535 173.580 1545 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.58 % Allowed : 26.94 % Favored : 63.47 % 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: 3.37 (0.24), residues: 990 helix: 2.53 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.20 (0.31), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 87 PHE 0.013 0.001 PHE M 112 ARG 0.006 0.002 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: D 65 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.7992 (p) REVERT: E 59 MET cc_start: 0.7695 (mtt) cc_final: 0.7427 (mtp) REVERT: E 94 LEU cc_start: 0.8899 (tp) cc_final: 0.8655 (tp) REVERT: J 54 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8091 (m) REVERT: K 54 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7997 (t) REVERT: K 59 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7646 (mtt) REVERT: M 54 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7692 (t) REVERT: N 54 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7796 (t) REVERT: N 93 SER cc_start: 0.8165 (t) cc_final: 0.7736 (p) REVERT: O 54 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7944 (t) outliers start: 69 outliers final: 40 residues processed: 218 average time/residue: 0.7887 time to fit residues: 186.4922 Evaluate side-chains 212 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 165 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7950 Z= 0.227 Angle : 0.593 8.296 10590 Z= 0.287 Chirality : 0.036 0.117 1230 Planarity : 0.006 0.071 1260 Dihedral : 30.500 173.738 1545 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.61 % Allowed : 28.61 % Favored : 62.78 % 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: 3.40 (0.24), residues: 990 helix: 2.57 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 87 PHE 0.011 0.001 PHE M 112 ARG 0.019 0.005 ARG J 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 180 time to evaluate : 0.781 Fit side-chains REVERT: D 65 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8007 (p) REVERT: E 94 LEU cc_start: 0.8875 (tp) cc_final: 0.8636 (tp) REVERT: J 54 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8088 (m) REVERT: K 54 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8004 (t) REVERT: K 59 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7648 (mtt) REVERT: M 54 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7681 (t) REVERT: N 54 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7795 (t) REVERT: O 54 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7914 (t) outliers start: 62 outliers final: 44 residues processed: 214 average time/residue: 0.6211 time to fit residues: 147.0301 Evaluate side-chains 218 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN G 62 ASN J 62 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7950 Z= 0.221 Angle : 0.587 8.126 10590 Z= 0.284 Chirality : 0.035 0.098 1230 Planarity : 0.004 0.049 1260 Dihedral : 29.515 174.856 1545 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.47 % Allowed : 28.19 % Favored : 63.33 % 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: 3.45 (0.24), residues: 990 helix: 2.62 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.62 (0.26), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 87 PHE 0.012 0.001 PHE F 89 ARG 0.015 0.004 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 177 time to evaluate : 0.694 Fit side-chains REVERT: A 65 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7992 (p) REVERT: D 65 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8009 (p) REVERT: E 94 LEU cc_start: 0.8857 (tp) cc_final: 0.8620 (tp) REVERT: H 74 SER cc_start: 0.8755 (m) cc_final: 0.8460 (p) REVERT: K 54 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (t) REVERT: K 59 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: L 60 VAL cc_start: 0.8553 (t) cc_final: 0.8244 (m) REVERT: N 54 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7785 (t) REVERT: O 60 VAL cc_start: 0.8323 (t) cc_final: 0.7996 (m) outliers start: 61 outliers final: 43 residues processed: 210 average time/residue: 0.6026 time to fit residues: 140.6083 Evaluate side-chains 214 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7950 Z= 0.211 Angle : 0.583 8.668 10590 Z= 0.282 Chirality : 0.035 0.110 1230 Planarity : 0.004 0.040 1260 Dihedral : 28.161 177.073 1545 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 7.08 % Allowed : 30.28 % Favored : 62.64 % 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: 3.50 (0.24), residues: 990 helix: 2.66 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 87 PHE 0.011 0.001 PHE M 112 ARG 0.013 0.003 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 0.809 Fit side-chains REVERT: A 65 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7999 (p) REVERT: D 65 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8020 (p) REVERT: E 94 LEU cc_start: 0.8861 (tp) cc_final: 0.8625 (tp) REVERT: E 115 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7415 (mttm) REVERT: H 74 SER cc_start: 0.8813 (m) cc_final: 0.8483 (p) REVERT: K 54 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (t) REVERT: K 59 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7612 (mtt) REVERT: L 60 VAL cc_start: 0.8482 (t) cc_final: 0.8184 (m) REVERT: N 54 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7788 (t) REVERT: O 60 VAL cc_start: 0.8310 (t) cc_final: 0.7991 (m) outliers start: 51 outliers final: 40 residues processed: 198 average time/residue: 0.6140 time to fit residues: 134.6238 Evaluate side-chains 212 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7950 Z= 0.239 Angle : 0.613 9.299 10590 Z= 0.295 Chirality : 0.036 0.136 1230 Planarity : 0.004 0.042 1260 Dihedral : 27.214 168.521 1545 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.22 % Allowed : 30.69 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.24), residues: 990 helix: 2.51 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 87 PHE 0.011 0.002 PHE M 112 ARG 0.011 0.003 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 0.844 Fit side-chains REVERT: A 65 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7995 (p) REVERT: D 65 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.7986 (p) REVERT: E 94 LEU cc_start: 0.8893 (tp) cc_final: 0.8664 (tp) REVERT: H 74 SER cc_start: 0.8822 (m) cc_final: 0.8485 (p) REVERT: K 54 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8054 (t) REVERT: K 59 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: N 54 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7813 (t) REVERT: O 60 VAL cc_start: 0.8329 (t) cc_final: 0.8008 (m) outliers start: 52 outliers final: 41 residues processed: 195 average time/residue: 0.6487 time to fit residues: 139.7574 Evaluate side-chains 207 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7950 Z= 0.234 Angle : 0.603 8.980 10590 Z= 0.291 Chirality : 0.036 0.146 1230 Planarity : 0.004 0.038 1260 Dihedral : 25.981 151.280 1545 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.08 % Allowed : 30.69 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.24), residues: 990 helix: 2.53 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 87 PHE 0.011 0.002 PHE M 112 ARG 0.009 0.002 ARG F 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 0.851 Fit side-chains REVERT: A 65 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7995 (p) REVERT: D 65 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7985 (p) REVERT: E 94 LEU cc_start: 0.8893 (tp) cc_final: 0.8661 (tp) REVERT: E 115 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7346 (mttm) REVERT: H 74 SER cc_start: 0.8816 (m) cc_final: 0.8482 (p) REVERT: K 54 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8035 (t) REVERT: K 59 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7662 (mtt) REVERT: N 54 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7802 (t) REVERT: O 60 VAL cc_start: 0.8319 (t) cc_final: 0.8002 (m) outliers start: 51 outliers final: 43 residues processed: 197 average time/residue: 0.6347 time to fit residues: 138.3878 Evaluate side-chains 212 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112239 restraints weight = 10491.335| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.20 r_work: 0.3194 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7950 Z= 0.231 Angle : 0.604 9.118 10590 Z= 0.291 Chirality : 0.036 0.148 1230 Planarity : 0.004 0.039 1260 Dihedral : 24.950 150.413 1545 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.08 % Allowed : 30.28 % Favored : 62.64 % 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: 3.22 (0.24), residues: 990 helix: 2.52 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -2.25 (0.22), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 87 PHE 0.010 0.001 PHE M 112 ARG 0.008 0.002 ARG N 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.35 seconds wall clock time: 50 minutes 2.24 seconds (3002.24 seconds total)