Starting phenix.real_space_refine on Wed Feb 12 09:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_28957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_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/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_28957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_28957.map" model { file = "/net/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_28957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fai_28957/02_2025/8fai_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-5592/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: 3.24, 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 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: 0.69 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: 2.55 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } 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: 1.740 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 18.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.676 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: 0.7316 time to fit residues: 215.8516 Evaluate side-chains 189 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114462 restraints weight = 10757.015| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.26 r_work: 0.3220 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.819 Fit side-chains REVERT: A 54 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7999 (t) REVERT: A 91 ARG cc_start: 0.6726 (ppt170) cc_final: 0.6510 (ppt170) REVERT: B 74 SER cc_start: 0.8974 (m) cc_final: 0.8516 (p) REVERT: C 54 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7978 (t) REVERT: C 74 SER cc_start: 0.8992 (m) cc_final: 0.8571 (p) REVERT: D 74 SER cc_start: 0.8976 (m) cc_final: 0.8603 (p) REVERT: F 54 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8099 (t) REVERT: G 54 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7951 (t) REVERT: H 54 THR cc_start: 0.8268 (p) cc_final: 0.7898 (t) REVERT: J 54 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7943 (t) REVERT: K 54 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7854 (t) REVERT: L 54 THR cc_start: 0.8216 (p) cc_final: 0.7917 (t) REVERT: M 54 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7960 (t) REVERT: N 54 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (t) REVERT: N 60 VAL cc_start: 0.8536 (t) cc_final: 0.7841 (m) REVERT: O 54 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7931 (t) outliers start: 49 outliers final: 28 residues processed: 223 average time/residue: 0.6275 time to fit residues: 154.9152 Evaluate side-chains 208 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113843 restraints weight = 10776.204| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.25 r_work: 0.3208 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2952 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= 0.230 Angle : 0.609 8.837 10590 Z= 0.295 Chirality : 0.037 0.206 1230 Planarity : 0.003 0.028 1260 Dihedral : 11.996 50.832 1815 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.22 % Allowed : 24.72 % Favored : 68.06 % 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: 3.75 (0.25), residues: 990 helix: 2.88 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 87 PHE 0.011 0.001 PHE K 112 ARG 0.008 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 226 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.787 Fit side-chains REVERT: A 54 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8013 (t) REVERT: B 54 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7921 (t) REVERT: C 54 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8043 (t) REVERT: D 65 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8175 (p) REVERT: E 59 MET cc_start: 0.7981 (mtt) cc_final: 0.7642 (mtp) REVERT: E 94 LEU cc_start: 0.8882 (tp) cc_final: 0.8655 (tp) REVERT: F 54 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8135 (t) REVERT: G 54 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8023 (t) REVERT: H 54 THR cc_start: 0.8299 (p) cc_final: 0.7953 (t) REVERT: H 74 SER cc_start: 0.8930 (m) cc_final: 0.8650 (p) REVERT: J 54 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8332 (m) REVERT: K 54 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (t) REVERT: L 54 THR cc_start: 0.8318 (p) cc_final: 0.8079 (t) REVERT: M 54 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7898 (t) REVERT: N 54 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8049 (t) REVERT: N 60 VAL cc_start: 0.8489 (t) cc_final: 0.8097 (m) REVERT: O 54 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (t) outliers start: 52 outliers final: 31 residues processed: 198 average time/residue: 0.6500 time to fit residues: 142.1186 Evaluate side-chains 211 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 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 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 I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 88 MET 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 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 Chi-restraints excluded: chain O residue 111 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN L 61 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115360 restraints weight = 10657.602| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.15 r_work: 0.3240 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3100 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= 0.201 Angle : 0.541 8.028 10590 Z= 0.267 Chirality : 0.035 0.140 1230 Planarity : 0.003 0.023 1260 Dihedral : 11.356 49.628 1815 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.61 % Allowed : 24.72 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.25), residues: 990 helix: 2.99 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.68 (0.30), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 87 PHE 0.008 0.001 PHE M 112 ARG 0.005 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 243 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: D 65 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8196 (p) REVERT: E 59 MET cc_start: 0.7955 (mtt) cc_final: 0.7717 (mtp) REVERT: E 94 LEU cc_start: 0.8876 (tp) cc_final: 0.8647 (tp) REVERT: E 115 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7506 (mttp) REVERT: G 54 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7989 (t) REVERT: G 88 MET cc_start: 0.7651 (ttm) cc_final: 0.7430 (ttp) REVERT: H 74 SER cc_start: 0.8876 (m) cc_final: 0.8621 (p) REVERT: K 54 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (t) REVERT: L 54 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8037 (t) REVERT: M 54 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7955 (t) REVERT: N 54 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8104 (t) REVERT: N 60 VAL cc_start: 0.8497 (t) cc_final: 0.8110 (m) REVERT: O 54 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8039 (t) outliers start: 62 outliers final: 34 residues processed: 210 average time/residue: 0.6320 time to fit residues: 146.5795 Evaluate side-chains 203 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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 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 96 LEU 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 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 74 optimal weight: 0.0060 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 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 = 0.3462 r_free = 0.3462 target = 0.124840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116191 restraints weight = 10641.940| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.15 r_work: 0.3255 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3221 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= 0.194 Angle : 0.537 8.560 10590 Z= 0.266 Chirality : 0.035 0.112 1230 Planarity : 0.003 0.046 1260 Dihedral : 11.245 55.401 1815 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 9.03 % Allowed : 26.53 % Favored : 64.44 % 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: 3.98 (0.25), residues: 990 helix: 3.06 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 87 PHE 0.008 0.001 PHE K 89 ARG 0.013 0.002 ARG K 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 238 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.766 Fit side-chains REVERT: E 59 MET cc_start: 0.7964 (mtt) cc_final: 0.7752 (mtp) REVERT: E 94 LEU cc_start: 0.8839 (tp) cc_final: 0.8623 (tp) REVERT: G 54 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7949 (t) REVERT: G 88 MET cc_start: 0.7634 (ttm) cc_final: 0.7414 (ttp) REVERT: H 74 SER cc_start: 0.8866 (m) cc_final: 0.8626 (p) REVERT: J 88 MET cc_start: 0.7941 (ttm) cc_final: 0.7608 (mtp) REVERT: L 54 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8020 (t) REVERT: M 54 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7927 (t) REVERT: M 60 VAL cc_start: 0.8550 (t) cc_final: 0.8198 (m) REVERT: N 54 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (t) REVERT: N 60 VAL cc_start: 0.8460 (t) cc_final: 0.7940 (m) outliers start: 65 outliers final: 41 residues processed: 211 average time/residue: 0.7552 time to fit residues: 173.7509 Evaluate side-chains 210 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 54 THR 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 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 F residue 97 VAL Chi-restraints excluded: chain G residue 54 THR 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 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 54 THR 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 111 SER Chi-restraints excluded: chain N residue 54 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113857 restraints weight = 10746.637| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.24 r_work: 0.3216 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3318 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= 0.255 Angle : 0.656 9.442 10590 Z= 0.316 Chirality : 0.037 0.104 1230 Planarity : 0.006 0.091 1260 Dihedral : 12.601 53.100 1815 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.19 % Allowed : 29.03 % 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: 3.75 (0.24), residues: 990 helix: 2.92 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 87 PHE 0.010 0.001 PHE F 89 ARG 0.019 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 235 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.750 Fit side-chains REVERT: D 65 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8204 (p) REVERT: E 59 MET cc_start: 0.8018 (mtt) cc_final: 0.7765 (mtp) REVERT: E 94 LEU cc_start: 0.8849 (tp) cc_final: 0.8632 (tp) REVERT: G 54 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8005 (t) REVERT: H 74 SER cc_start: 0.8965 (m) cc_final: 0.8694 (p) REVERT: L 54 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8019 (t) REVERT: N 54 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (t) REVERT: N 60 VAL cc_start: 0.8534 (t) cc_final: 0.8148 (m) outliers start: 59 outliers final: 46 residues processed: 207 average time/residue: 0.5955 time to fit residues: 137.1146 Evaluate side-chains 219 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 65 THR 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 54 THR Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 83 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 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 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 54 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN G 62 ASN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117509 restraints weight = 10700.077| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.13 r_work: 0.3259 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3395 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= 0.217 Angle : 0.597 8.613 10590 Z= 0.292 Chirality : 0.036 0.093 1230 Planarity : 0.004 0.048 1260 Dihedral : 11.881 50.846 1815 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.36 % Allowed : 29.86 % 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: 3.88 (0.24), residues: 990 helix: 3.02 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.97 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 87 PHE 0.007 0.001 PHE O 112 ARG 0.014 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 223 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.799 Fit side-chains REVERT: A 65 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8086 (p) REVERT: E 94 LEU cc_start: 0.8843 (tp) cc_final: 0.8640 (tp) REVERT: G 54 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.7979 (t) REVERT: H 74 SER cc_start: 0.8845 (m) cc_final: 0.8624 (p) REVERT: N 54 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8035 (t) REVERT: N 60 VAL cc_start: 0.8476 (t) cc_final: 0.8097 (m) outliers start: 53 outliers final: 42 residues processed: 202 average time/residue: 0.6316 time to fit residues: 141.8754 Evaluate side-chains 207 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 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 F residue 93 SER 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.122238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113021 restraints weight = 10743.868| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.27 r_work: 0.3197 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3359 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= 0.265 Angle : 0.663 10.027 10590 Z= 0.318 Chirality : 0.038 0.110 1230 Planarity : 0.004 0.041 1260 Dihedral : 12.928 58.452 1815 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.06 % Allowed : 29.72 % 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: 3.66 (0.24), residues: 990 helix: 2.87 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 87 PHE 0.009 0.001 PHE A 108 ARG 0.011 0.003 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 217 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 0.741 Fit side-chains REVERT: D 65 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8210 (p) REVERT: E 94 LEU cc_start: 0.8866 (tp) cc_final: 0.8650 (tp) REVERT: G 54 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8048 (t) REVERT: H 74 SER cc_start: 0.8909 (m) cc_final: 0.8631 (p) REVERT: N 54 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8076 (t) REVERT: N 60 VAL cc_start: 0.8551 (t) cc_final: 0.8156 (m) outliers start: 58 outliers final: 48 residues processed: 197 average time/residue: 0.6500 time to fit residues: 141.0920 Evaluate side-chains 209 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 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 65 THR 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 54 THR Chi-restraints excluded: chain G residue 83 ILE 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 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 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 59 MET 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 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 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114088 restraints weight = 10753.413| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.27 r_work: 0.3212 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7950 Z= 0.243 Angle : 0.633 9.565 10590 Z= 0.307 Chirality : 0.037 0.116 1230 Planarity : 0.004 0.039 1260 Dihedral : 12.605 53.442 1815 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.50 % Allowed : 30.14 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.24), residues: 990 helix: 2.90 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 87 PHE 0.008 0.001 PHE B 108 ARG 0.010 0.003 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 217 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8101 (p) REVERT: D 65 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8246 (p) REVERT: E 94 LEU cc_start: 0.8875 (tp) cc_final: 0.8660 (tp) REVERT: G 54 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8037 (t) REVERT: H 74 SER cc_start: 0.8903 (m) cc_final: 0.8645 (p) REVERT: N 54 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8072 (t) REVERT: N 60 VAL cc_start: 0.8535 (t) cc_final: 0.8144 (m) outliers start: 54 outliers final: 47 residues processed: 199 average time/residue: 0.6334 time to fit residues: 139.2253 Evaluate side-chains 211 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 88 MET 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 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 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 F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 91 ARG 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 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 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 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 83 ILE 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 4 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN F 62 ASN L 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116049 restraints weight = 10710.285| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.26 r_work: 0.3243 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3502 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= 0.211 Angle : 0.593 8.764 10590 Z= 0.291 Chirality : 0.036 0.131 1230 Planarity : 0.003 0.036 1260 Dihedral : 11.908 51.311 1815 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.94 % Allowed : 30.97 % 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: 3.89 (0.24), residues: 990 helix: 3.03 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.04 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 87 PHE 0.008 0.001 PHE N 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 214 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8112 (p) REVERT: D 65 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8242 (p) REVERT: G 54 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8025 (t) REVERT: H 74 SER cc_start: 0.8833 (m) cc_final: 0.8621 (p) REVERT: N 60 VAL cc_start: 0.8476 (t) cc_final: 0.8089 (m) outliers start: 50 outliers final: 44 residues processed: 197 average time/residue: 0.6446 time to fit residues: 140.1024 Evaluate side-chains 204 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 93 SER 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 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 F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 91 ARG 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 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 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 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 83 ILE 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 28 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114845 restraints weight = 10902.830| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.25 r_work: 0.3233 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7950 Z= 0.223 Angle : 0.609 9.154 10590 Z= 0.297 Chirality : 0.036 0.139 1230 Planarity : 0.003 0.033 1260 Dihedral : 12.054 52.132 1815 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 6.81 % Allowed : 31.81 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.24), residues: 990 helix: 3.00 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.06 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 87 PHE 0.007 0.001 PHE B 108 ARG 0.008 0.002 ARG O 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4582.30 seconds wall clock time: 81 minutes 33.11 seconds (4893.11 seconds total)