Starting phenix.real_space_refine on Tue Sep 24 09:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fai_28957/09_2024/8fai_28957.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7845 Number of models: 1 Model: "" Number of chains: 5 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: "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: "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: "G" 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} Restraints were copied for chains: C, B, E, D, F, I, H, J, M, L, O, N Time building chain proxies: 3.20, per 1000 atoms: 0.41 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 - 3.00 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 60 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 69 through 89 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 69 through 89 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 69 through 89 Processing helix chain 'C' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 69 through 89 Processing helix chain 'D' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 69 through 89 Processing helix chain 'E' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'F' and resid 55 through 68 Processing helix chain 'F' and resid 69 through 89 Processing helix chain 'F' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'G' and resid 55 through 68 Processing helix chain 'G' and resid 69 through 89 Processing helix chain 'G' and resid 93 through 109 removed outlier: 3.752A pdb=" N VAL G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'H' and resid 55 through 68 Processing helix chain 'H' and resid 69 through 89 Processing helix chain 'H' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 69 through 89 Processing helix chain 'J' and resid 93 through 109 removed outlier: 3.752A pdb=" N VAL J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'K' and resid 55 through 68 Processing helix chain 'K' and resid 69 through 89 Processing helix chain 'K' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL K 97 " --> pdb=" O SER K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'L' and resid 69 through 89 Processing helix chain 'L' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL L 97 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'M' and resid 55 through 68 Processing helix chain 'M' and resid 69 through 89 Processing helix chain 'M' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL M 97 " --> pdb=" O SER M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 Processing helix chain 'N' and resid 55 through 68 Processing helix chain 'N' and resid 69 through 89 Processing helix chain 'N' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL N 97 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 118 Processing helix chain 'O' and resid 55 through 68 Processing helix chain 'O' and resid 69 through 89 Processing helix chain 'O' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL O 97 " --> pdb=" O SER O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 118 675 hydrogen bonds defined for protein. 2025 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: 2.25 Time building geometry restraints manager: 2.51 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=" C31 XL0 L 202 " pdb=" O31 XL0 L 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C31 XL0 I 200 " pdb=" O31 XL0 I 200 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C31 XL0 M 202 " pdb=" O31 XL0 M 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C31 XL0 N 202 " pdb=" O31 XL0 N 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C31 XL0 N 201 " pdb=" O31 XL0 N 201 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 7945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 10249 4.47 - 8.94: 311 8.94 - 13.41: 15 13.41 - 17.88: 0 17.88 - 22.36: 15 Bond angle restraints: 10590 Sorted by residual: angle pdb=" O13 XL0 M 202 " pdb=" P XL0 M 202 " pdb=" O14 XL0 M 202 " ideal model delta sigma weight residual 123.28 100.92 22.36 3.00e+00 1.11e-01 5.55e+01 angle pdb=" O13 XL0 K 202 " pdb=" P XL0 K 202 " pdb=" O14 XL0 K 202 " ideal model delta sigma weight residual 123.28 100.93 22.35 3.00e+00 1.11e-01 5.55e+01 angle pdb=" O13 XL0 K 201 " pdb=" P XL0 K 201 " pdb=" O14 XL0 K 201 " ideal model delta sigma weight residual 123.28 100.94 22.34 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O13 XL0 H 200 " pdb=" P XL0 H 200 " pdb=" O14 XL0 H 200 " ideal model delta sigma weight residual 123.28 100.94 22.34 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O13 XL0 N 202 " pdb=" P XL0 N 202 " pdb=" O14 XL0 N 202 " ideal model delta sigma weight residual 123.28 100.95 22.33 3.00e+00 1.11e-01 5.54e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.75: 3651 10.75 - 21.50: 481 21.50 - 32.26: 443 32.26 - 43.01: 150 43.01 - 53.76: 45 Dihedral angle restraints: 4770 sinusoidal: 2145 harmonic: 2625 Sorted by residual: dihedral pdb=" CB MET N 59 " pdb=" CG MET N 59 " pdb=" SD MET N 59 " pdb=" CE MET N 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.01 38.99 3 1.50e+01 4.44e-03 6.89e+00 dihedral pdb=" CB MET B 59 " pdb=" CG MET B 59 " pdb=" SD MET B 59 " pdb=" CE MET B 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.01 38.99 3 1.50e+01 4.44e-03 6.89e+00 dihedral pdb=" CB MET I 59 " pdb=" CG MET I 59 " pdb=" SD MET I 59 " pdb=" CE MET I 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.02 38.98 3 1.50e+01 4.44e-03 6.89e+00 ... (remaining 4767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.053: 284 0.053 - 0.080: 211 0.080 - 0.106: 15 0.106 - 0.133: 15 Chirality restraints: 1230 Sorted by residual: chirality pdb=" C12 XL0 L 201 " pdb=" C11 XL0 L 201 " pdb=" C13 XL0 L 201 " pdb=" OC2 XL0 L 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.52 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" C12 XL0 F 200 " pdb=" C11 XL0 F 200 " pdb=" C13 XL0 F 200 " pdb=" OC2 XL0 F 200 " both_signs ideal model delta sigma weight residual False -2.38 -2.52 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" C12 XL0 O 201 " pdb=" C11 XL0 O 201 " pdb=" C13 XL0 O 201 " pdb=" OC2 XL0 O 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.51 0.13 2.00e-01 2.50e+01 4.23e-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: 2815 2.90 - 3.40: 8045 3.40 - 3.90: 13421 3.90 - 4.40: 15033 4.40 - 4.90: 23836 Nonbonded interactions: 63150 Sorted by model distance: nonbonded pdb=" O LEU B 117 " pdb=" OG1 THR B 118 " model vdw 2.395 3.040 nonbonded pdb=" O LEU N 117 " pdb=" OG1 THR N 118 " model vdw 2.395 3.040 nonbonded pdb=" O LEU G 117 " pdb=" OG1 THR G 118 " model vdw 2.396 3.040 nonbonded pdb=" O LEU A 117 " pdb=" OG1 THR A 118 " model vdw 2.396 3.040 nonbonded pdb=" O LEU K 117 " pdb=" OG1 THR K 118 " model vdw 2.396 3.040 ... (remaining 63145 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 '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: 1.430 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.850 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- 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 : 0.011 0.107 7950 Z= 0.713 Angle : 1.627 22.356 10590 Z= 0.588 Chirality : 0.038 0.133 1230 Planarity : 0.004 0.022 1260 Dihedral : 15.884 53.761 3150 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 : 0.763 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: 0.7121 time to fit residues: 210.8358 Evaluate side-chains 189 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 0.6980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7950 Z= 0.239 Angle : 0.658 8.382 10590 Z= 0.321 Chirality : 0.038 0.211 1230 Planarity : 0.005 0.044 1260 Dihedral : 12.494 45.850 1818 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 6.81 % Allowed : 22.08 % Favored : 71.11 % 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: 3.76 (0.26), residues: 990 helix: 2.88 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 87 PHE 0.012 0.001 PHE L 112 ARG 0.014 0.003 ARG N 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: 49 poor density : 202 time to evaluate : 0.773 Fit side-chains REVERT: A 54 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 74 SER cc_start: 0.8789 (m) cc_final: 0.8243 (p) REVERT: C 54 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7856 (t) REVERT: C 74 SER cc_start: 0.8861 (m) cc_final: 0.8377 (p) REVERT: D 74 SER cc_start: 0.8836 (m) cc_final: 0.8397 (p) REVERT: F 54 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7998 (t) REVERT: G 54 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7794 (t) REVERT: H 54 THR cc_start: 0.8166 (p) cc_final: 0.7800 (t) REVERT: J 54 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7811 (t) REVERT: K 54 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (t) REVERT: L 54 THR cc_start: 0.8045 (p) cc_final: 0.7742 (t) REVERT: L 64 CYS cc_start: 0.7714 (m) cc_final: 0.7485 (m) REVERT: M 54 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7800 (t) REVERT: N 54 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7582 (t) REVERT: N 60 VAL cc_start: 0.8428 (t) cc_final: 0.7677 (m) REVERT: O 54 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (t) outliers start: 49 outliers final: 28 residues processed: 223 average time/residue: 0.6053 time to fit residues: 150.1501 Evaluate side-chains 208 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 93 SER 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: 0.7980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN L 61 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7950 Z= 0.187 Angle : 0.541 7.424 10590 Z= 0.270 Chirality : 0.035 0.203 1230 Planarity : 0.003 0.024 1260 Dihedral : 10.749 41.621 1815 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 25.83 % Favored : 67.92 % 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: 4.01 (0.25), residues: 990 helix: 3.06 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 87 PHE 0.010 0.001 PHE K 112 ARG 0.007 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 211 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 0.747 Fit side-chains REVERT: A 54 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7841 (t) REVERT: B 54 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7770 (t) REVERT: B 59 MET cc_start: 0.7490 (mtp) cc_final: 0.7284 (mtt) REVERT: E 54 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8007 (t) REVERT: E 59 MET cc_start: 0.7600 (mtt) cc_final: 0.7365 (mtt) REVERT: E 115 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7412 (mttm) REVERT: F 54 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8072 (t) REVERT: G 54 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7862 (t) REVERT: G 88 MET cc_start: 0.7490 (ttm) cc_final: 0.7264 (ttp) REVERT: H 54 THR cc_start: 0.8197 (p) cc_final: 0.7833 (t) REVERT: H 74 SER cc_start: 0.8706 (m) cc_final: 0.8435 (p) REVERT: J 54 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7988 (t) REVERT: K 54 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7963 (t) REVERT: L 54 THR cc_start: 0.8129 (p) cc_final: 0.7889 (t) REVERT: L 64 CYS cc_start: 0.7600 (m) cc_final: 0.7373 (m) REVERT: M 54 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7798 (t) REVERT: M 60 VAL cc_start: 0.8415 (t) cc_final: 0.7738 (m) REVERT: N 54 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7863 (t) REVERT: N 60 VAL cc_start: 0.8306 (t) cc_final: 0.7955 (m) REVERT: O 54 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7911 (t) outliers start: 45 outliers final: 22 residues processed: 184 average time/residue: 0.6555 time to fit residues: 133.2234 Evaluate side-chains 194 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR 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 97 VAL 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 M residue 111 SER 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: 0.9980 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3065 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= 0.219 Angle : 0.570 8.828 10590 Z= 0.278 Chirality : 0.036 0.091 1230 Planarity : 0.003 0.023 1260 Dihedral : 11.789 51.907 1815 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.78 % Allowed : 26.25 % Favored : 65.97 % 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: 3.95 (0.25), residues: 990 helix: 2.92 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.07 (0.33), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 87 PHE 0.009 0.001 PHE M 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 230 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 0.781 Fit side-chains REVERT: B 54 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7917 (t) REVERT: D 65 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8099 (p) REVERT: E 59 MET cc_start: 0.7681 (mtt) cc_final: 0.7388 (mtp) REVERT: E 115 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7417 (mttp) REVERT: G 54 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7828 (t) REVERT: K 54 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8038 (t) REVERT: L 54 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7901 (t) REVERT: L 64 CYS cc_start: 0.7725 (m) cc_final: 0.7511 (m) REVERT: M 54 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7834 (t) REVERT: N 54 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7956 (t) REVERT: N 60 VAL cc_start: 0.8386 (t) cc_final: 0.8029 (m) REVERT: O 54 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7932 (t) outliers start: 56 outliers final: 32 residues processed: 199 average time/residue: 0.5747 time to fit residues: 127.6345 Evaluate side-chains 201 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR 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 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR 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 G residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 67 ILE 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 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 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 93 SER 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: 0.7980 chunk 64 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN E 62 ASN J 62 ASN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3192 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= 0.192 Angle : 0.521 8.377 10590 Z= 0.258 Chirality : 0.035 0.092 1230 Planarity : 0.003 0.019 1260 Dihedral : 11.126 49.233 1815 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 8.06 % Allowed : 27.36 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.25), residues: 990 helix: 3.12 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 87 PHE 0.008 0.001 PHE O 112 ARG 0.005 0.001 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 236 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 0.776 Fit side-chains REVERT: E 59 MET cc_start: 0.7641 (mtt) cc_final: 0.7410 (mtp) REVERT: E 115 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7361 (mttp) REVERT: G 54 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7817 (t) REVERT: H 74 SER cc_start: 0.8741 (m) cc_final: 0.8465 (p) REVERT: K 54 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8036 (t) REVERT: L 54 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7889 (t) REVERT: L 64 CYS cc_start: 0.7627 (m) cc_final: 0.7425 (m) REVERT: M 54 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7811 (t) REVERT: M 60 VAL cc_start: 0.8381 (t) cc_final: 0.8034 (m) REVERT: N 54 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (t) REVERT: N 60 VAL cc_start: 0.8342 (t) cc_final: 0.7804 (m) outliers start: 58 outliers final: 30 residues processed: 212 average time/residue: 0.7309 time to fit residues: 168.8650 Evaluate side-chains 198 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 58 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR 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 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 M residue 111 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 62 ASN F 62 ASN G 62 ASN L 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7950 Z= 0.204 Angle : 0.597 8.505 10590 Z= 0.292 Chirality : 0.036 0.093 1230 Planarity : 0.006 0.090 1260 Dihedral : 11.667 49.110 1815 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 29.86 % Favored : 63.89 % 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: 4.08 (0.25), residues: 990 helix: 3.03 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 87 PHE 0.008 0.001 PHE F 89 ARG 0.021 0.004 ARG O 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 218 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 0.694 Fit side-chains REVERT: E 59 MET cc_start: 0.7628 (mtt) cc_final: 0.7375 (mtp) REVERT: G 54 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7831 (t) REVERT: H 74 SER cc_start: 0.8743 (m) cc_final: 0.8447 (p) REVERT: M 60 VAL cc_start: 0.8379 (t) cc_final: 0.7877 (m) REVERT: N 54 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7914 (t) REVERT: N 60 VAL cc_start: 0.8302 (t) cc_final: 0.7952 (m) outliers start: 45 outliers final: 34 residues processed: 199 average time/residue: 0.5804 time to fit residues: 129.5827 Evaluate side-chains 199 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR 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 97 VAL 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 86 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 93 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 62 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7950 Z= 0.190 Angle : 0.561 7.847 10590 Z= 0.277 Chirality : 0.035 0.090 1230 Planarity : 0.003 0.044 1260 Dihedral : 11.015 52.224 1815 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 31.25 % Favored : 62.50 % 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: 4.16 (0.24), residues: 990 helix: 3.09 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 87 PHE 0.008 0.001 PHE O 112 ARG 0.013 0.003 ARG O 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 214 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 0.845 Fit side-chains REVERT: A 65 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8047 (p) REVERT: D 74 SER cc_start: 0.8760 (m) cc_final: 0.8357 (p) REVERT: E 59 MET cc_start: 0.7613 (mtt) cc_final: 0.7352 (mtp) REVERT: G 54 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7779 (t) REVERT: H 74 SER cc_start: 0.8745 (m) cc_final: 0.8448 (p) REVERT: M 60 VAL cc_start: 0.8391 (t) cc_final: 0.8068 (m) outliers start: 45 outliers final: 35 residues processed: 197 average time/residue: 0.6836 time to fit residues: 150.8395 Evaluate side-chains 195 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 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 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 54 THR 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 97 VAL Chi-restraints excluded: chain K residue 67 ILE 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 86 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 93 SER 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7950 Z= 0.214 Angle : 0.592 8.701 10590 Z= 0.289 Chirality : 0.036 0.109 1230 Planarity : 0.003 0.036 1260 Dihedral : 11.517 55.096 1815 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 31.81 % Favored : 61.94 % 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: 4.04 (0.24), residues: 990 helix: 3.01 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 87 PHE 0.011 0.001 PHE L 112 ARG 0.009 0.002 ARG O 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 207 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 0.780 Fit side-chains REVERT: A 65 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 58 THR cc_start: 0.7766 (p) cc_final: 0.7457 (t) REVERT: G 54 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7804 (t) REVERT: H 74 SER cc_start: 0.8830 (m) cc_final: 0.8490 (p) REVERT: N 60 VAL cc_start: 0.8298 (t) cc_final: 0.7994 (m) outliers start: 45 outliers final: 40 residues processed: 191 average time/residue: 0.5918 time to fit residues: 125.8176 Evaluate side-chains 200 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 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 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR 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 67 ILE 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 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 97 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 SER 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: 0.6980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7950 Z= 0.241 Angle : 0.627 9.517 10590 Z= 0.303 Chirality : 0.037 0.116 1230 Planarity : 0.004 0.037 1260 Dihedral : 12.136 53.933 1815 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.53 % Allowed : 31.39 % 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: 3.87 (0.24), residues: 990 helix: 2.90 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 87 PHE 0.012 0.001 PHE L 112 ARG 0.009 0.002 ARG O 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 210 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 0.709 Fit side-chains REVERT: A 65 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 58 THR cc_start: 0.7806 (p) cc_final: 0.7517 (t) REVERT: E 59 MET cc_start: 0.7449 (mtp) cc_final: 0.7187 (mtp) REVERT: G 54 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7803 (t) REVERT: H 74 SER cc_start: 0.8880 (m) cc_final: 0.8508 (p) REVERT: N 60 VAL cc_start: 0.8332 (t) cc_final: 0.8009 (m) outliers start: 47 outliers final: 41 residues processed: 194 average time/residue: 0.5807 time to fit residues: 125.4389 Evaluate side-chains 205 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 86 SER 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 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 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 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 VAL 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 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 83 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 97 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 SER 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: 0.7980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN L 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7950 Z= 0.215 Angle : 0.592 8.870 10590 Z= 0.290 Chirality : 0.037 0.141 1230 Planarity : 0.003 0.035 1260 Dihedral : 11.678 53.207 1815 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.39 % Allowed : 32.08 % Favored : 61.53 % 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: 3.95 (0.24), residues: 990 helix: 2.95 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 87 PHE 0.024 0.001 PHE L 112 ARG 0.009 0.002 ARG O 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 209 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 163 time to evaluate : 0.894 Fit side-chains REVERT: A 65 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 58 THR cc_start: 0.7719 (p) cc_final: 0.7438 (t) REVERT: E 59 MET cc_start: 0.7447 (mtp) cc_final: 0.7193 (mtp) REVERT: G 54 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7821 (t) REVERT: H 74 SER cc_start: 0.8699 (m) cc_final: 0.8446 (p) REVERT: L 112 PHE cc_start: 0.7099 (m-80) cc_final: 0.6590 (m-10) REVERT: N 60 VAL cc_start: 0.8281 (t) cc_final: 0.7974 (m) outliers start: 46 outliers final: 43 residues processed: 194 average time/residue: 0.5958 time to fit residues: 128.5654 Evaluate side-chains 204 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 86 SER 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 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 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 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 G residue 97 VAL 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 67 ILE 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 83 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 97 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 SER 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 65 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114355 restraints weight = 10710.867| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.24 r_work: 0.3227 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7950 Z= 0.236 Angle : 0.621 9.432 10590 Z= 0.301 Chirality : 0.037 0.147 1230 Planarity : 0.003 0.035 1260 Dihedral : 12.098 53.609 1815 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 6.94 % Allowed : 31.53 % Favored : 61.53 % 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: 3.85 (0.24), residues: 990 helix: 2.89 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.56 (0.27), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 87 PHE 0.021 0.001 PHE L 112 ARG 0.009 0.002 ARG O 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.10 seconds wall clock time: 49 minutes 9.69 seconds (2949.69 seconds total)