Starting phenix.real_space_refine on Sat Apr 26 15:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlw_36406/04_2025/8jlw_36406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlw_36406/04_2025/8jlw_36406.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/8jlw_36406/04_2025/8jlw_36406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlw_36406/04_2025/8jlw_36406.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlw_36406/04_2025/8jlw_36406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlw_36406/04_2025/8jlw_36406.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= 0.037 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 1352 2.51 5 N 364 2.21 5 O 422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 424 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain breaks: 2 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 2.76, per 1000 atoms: 1.28 Number of scatterers: 2157 At special positions: 0 Unit cell: (55.1, 66.5, 77.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 422 8.00 N 364 7.00 C 1352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1198 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1205 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1207 " distance=2.03 Simple disulfide: pdb=" SG CYS A1193 " - pdb=" SG CYS A1360 " distance=2.02 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1368 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 258.1 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 7 sheets defined 1.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1162 through 1164 removed outlier: 3.595A pdb=" N CYS A1205 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.751A pdb=" N SER H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.043A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.626A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 165 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: 0.53 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 679 1.34 - 1.46: 607 1.46 - 1.58: 906 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 2216 Sorted by residual: bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.22e+00 bond pdb=" CB CYS H 96 " pdb=" SG CYS H 96 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CB VAL A1201 " pdb=" CG2 VAL A1201 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB LYS H 63 " pdb=" CG LYS H 63 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.43e-01 bond pdb=" CA SER L 49 " pdb=" CB SER L 49 " ideal model delta sigma weight residual 1.536 1.516 0.020 2.08e-02 2.31e+03 9.11e-01 ... (remaining 2211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 2860 1.46 - 2.93: 121 2.93 - 4.39: 18 4.39 - 5.85: 2 5.85 - 7.31: 2 Bond angle restraints: 3003 Sorted by residual: angle pdb=" C CYS A1193 " pdb=" N ASN A1194 " pdb=" CA ASN A1194 " ideal model delta sigma weight residual 120.97 128.24 -7.27 2.84e+00 1.24e-01 6.56e+00 angle pdb=" CB LYS H 63 " pdb=" CG LYS H 63 " pdb=" CD LYS H 63 " ideal model delta sigma weight residual 111.30 116.69 -5.39 2.30e+00 1.89e-01 5.50e+00 angle pdb=" C GLN H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.09e+00 angle pdb=" CA ILE L 94 " pdb=" C ILE L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 118.88 122.25 -3.37 1.54e+00 4.22e-01 4.78e+00 angle pdb=" C HIS L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.65e+00 ... (remaining 2998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1136 15.98 - 31.95: 121 31.95 - 47.92: 30 47.92 - 63.90: 11 63.90 - 79.87: 2 Dihedral angle restraints: 1300 sinusoidal: 508 harmonic: 792 Sorted by residual: dihedral pdb=" CB CYS A1169 " pdb=" SG CYS A1169 " pdb=" SG CYS A1205 " pdb=" CB CYS A1205 " ideal model delta sinusoidal sigma weight residual 93.00 31.75 61.25 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CA ASN L 28 " pdb=" C ASN L 28 " pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 59.66 33.34 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 1297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 219 0.041 - 0.083: 68 0.083 - 0.124: 20 0.124 - 0.165: 1 0.165 - 0.206: 1 Chirality restraints: 309 Sorted by residual: chirality pdb=" CB ILE L 94 " pdb=" CA ILE L 94 " pdb=" CG1 ILE L 94 " pdb=" CG2 ILE L 94 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 306 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO L 8 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1194 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A1195 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A1195 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1195 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO H 14 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.022 5.00e-02 4.00e+02 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 499 2.78 - 3.31: 1850 3.31 - 3.84: 3402 3.84 - 4.37: 4093 4.37 - 4.90: 7323 Nonbonded interactions: 17167 Sorted by model distance: nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.255 3.040 nonbonded pdb=" O PRO H 7 " pdb=" OG1 THR H 113 " model vdw 2.273 3.040 nonbonded pdb=" ND2 ASN A1194 " pdb=" O CYS A1198 " model vdw 2.316 3.120 nonbonded pdb=" ND2 ASN H 55 " pdb=" OD2 ASP H 57 " model vdw 2.321 3.120 nonbonded pdb=" O TRP H 47 " pdb=" ND2 ASN H 61 " model vdw 2.335 3.120 ... (remaining 17162 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.310 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:15.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2223 Z= 0.199 Angle : 0.702 7.315 3017 Z= 0.376 Chirality : 0.043 0.206 309 Planarity : 0.006 0.073 384 Dihedral : 14.614 79.870 779 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.52), residues: 270 helix: None (None), residues: 0 sheet: -0.65 (0.50), residues: 122 loop : -1.55 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1197 HIS 0.006 0.002 HIS L 90 PHE 0.008 0.001 PHE L 98 TYR 0.014 0.003 TYR A1359 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.14662 ( 65) hydrogen bonds : angle 8.30483 ( 165) SS BOND : bond 0.00533 ( 7) SS BOND : angle 1.66062 ( 14) covalent geometry : bond 0.00453 ( 2216) covalent geometry : angle 0.69427 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.238 Fit side-chains REVERT: H 39 GLN cc_start: 0.7078 (pt0) cc_final: 0.6314 (tt0) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 1.1620 time to fit residues: 51.1550 Evaluate side-chains 34 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.211881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.191581 restraints weight = 2479.689| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.17 r_work: 0.4084 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2223 Z= 0.155 Angle : 0.662 6.946 3017 Z= 0.349 Chirality : 0.043 0.222 309 Planarity : 0.005 0.048 384 Dihedral : 5.991 21.205 301 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.86 % Allowed : 11.59 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.52), residues: 270 helix: None (None), residues: 0 sheet: -0.32 (0.54), residues: 112 loop : -1.68 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 109 HIS 0.004 0.001 HIS L 91 PHE 0.008 0.001 PHE H 29 TYR 0.012 0.002 TYR H 95 ARG 0.002 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 65) hydrogen bonds : angle 6.70171 ( 165) SS BOND : bond 0.00427 ( 7) SS BOND : angle 1.46058 ( 14) covalent geometry : bond 0.00358 ( 2216) covalent geometry : angle 0.65564 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7398 (pt0) cc_final: 0.6653 (tt0) REVERT: L 81 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7241 (mt-10) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 1.1910 time to fit residues: 49.9860 Evaluate side-chains 39 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 chunk 17 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.1522 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.216622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196444 restraints weight = 2498.914| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.16 r_work: 0.4125 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2223 Z= 0.106 Angle : 0.585 6.398 3017 Z= 0.306 Chirality : 0.042 0.244 309 Planarity : 0.004 0.046 384 Dihedral : 5.392 20.495 301 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.86 % Allowed : 14.59 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.01 (0.53), residues: 120 loop : -1.63 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.003 0.001 HIS L 91 PHE 0.005 0.001 PHE L 71 TYR 0.011 0.001 TYR H 95 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 65) hydrogen bonds : angle 5.99343 ( 165) SS BOND : bond 0.00259 ( 7) SS BOND : angle 0.77004 ( 14) covalent geometry : bond 0.00235 ( 2216) covalent geometry : angle 0.58413 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7171 (pt0) cc_final: 0.6750 (tt0) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 1.1840 time to fit residues: 49.6589 Evaluate side-chains 34 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0010 chunk 1 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.2990 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.214018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193889 restraints weight = 2449.185| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.09 r_work: 0.4110 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2223 Z= 0.126 Angle : 0.607 7.019 3017 Z= 0.320 Chirality : 0.043 0.248 309 Planarity : 0.005 0.049 384 Dihedral : 5.475 19.960 301 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.58 % Allowed : 13.73 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.00 (0.53), residues: 120 loop : -1.56 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.004 0.001 HIS L 91 PHE 0.005 0.001 PHE L 98 TYR 0.011 0.002 TYR H 94 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 65) hydrogen bonds : angle 5.96513 ( 165) SS BOND : bond 0.00297 ( 7) SS BOND : angle 1.03472 ( 14) covalent geometry : bond 0.00289 ( 2216) covalent geometry : angle 0.60468 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5868 (mtm180) REVERT: L 81 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7575 (mm-30) outliers start: 6 outliers final: 1 residues processed: 40 average time/residue: 1.2939 time to fit residues: 52.8858 Evaluate side-chains 35 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.207886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.188442 restraints weight = 2464.433| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.04 r_work: 0.4058 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2223 Z= 0.187 Angle : 0.666 7.258 3017 Z= 0.352 Chirality : 0.044 0.232 309 Planarity : 0.005 0.055 384 Dihedral : 5.816 20.284 301 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.00 % Allowed : 14.16 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.03 (0.52), residues: 119 loop : -1.43 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1197 HIS 0.004 0.002 HIS L 91 PHE 0.008 0.001 PHE L 98 TYR 0.014 0.003 TYR H 94 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 65) hydrogen bonds : angle 6.42040 ( 165) SS BOND : bond 0.00484 ( 7) SS BOND : angle 1.40628 ( 14) covalent geometry : bond 0.00436 ( 2216) covalent geometry : angle 0.66082 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: L 61 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5865 (mtm180) REVERT: L 81 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7370 (mt-10) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 1.2704 time to fit residues: 51.9755 Evaluate side-chains 37 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.214750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195107 restraints weight = 2498.511| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.11 r_work: 0.4110 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2223 Z= 0.118 Angle : 0.619 6.907 3017 Z= 0.322 Chirality : 0.043 0.259 309 Planarity : 0.005 0.053 384 Dihedral : 5.499 20.399 301 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.72 % Allowed : 17.17 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.04 (0.52), residues: 121 loop : -1.39 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.004 0.001 HIS L 91 PHE 0.005 0.001 PHE L 71 TYR 0.021 0.002 TYR H 95 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02658 ( 65) hydrogen bonds : angle 5.85000 ( 165) SS BOND : bond 0.00313 ( 7) SS BOND : angle 1.20715 ( 14) covalent geometry : bond 0.00273 ( 2216) covalent geometry : angle 0.61444 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 1359 TYR cc_start: 0.7628 (p90) cc_final: 0.7371 (p90) REVERT: H 39 GLN cc_start: 0.6738 (pt0) cc_final: 0.6351 (mt0) REVERT: L 81 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7552 (mm-30) outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 1.2490 time to fit residues: 49.7922 Evaluate side-chains 32 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 overall best weight: 0.1186 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.220597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.201343 restraints weight = 2499.921| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.10 r_work: 0.4171 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2223 Z= 0.113 Angle : 0.642 7.186 3017 Z= 0.332 Chirality : 0.043 0.257 309 Planarity : 0.005 0.049 384 Dihedral : 5.389 28.308 301 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.29 % Allowed : 18.03 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.53), residues: 270 helix: None (None), residues: 0 sheet: 0.07 (0.53), residues: 121 loop : -1.62 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.003 0.001 HIS L 91 PHE 0.005 0.001 PHE H 106 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.02496 ( 65) hydrogen bonds : angle 5.37289 ( 165) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.65963 ( 14) covalent geometry : bond 0.00270 ( 2216) covalent geometry : angle 0.63326 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.6584 (pt0) cc_final: 0.6243 (mt0) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 1.1546 time to fit residues: 44.9396 Evaluate side-chains 33 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.211017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191180 restraints weight = 2523.930| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.11 r_work: 0.4077 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2223 Z= 0.204 Angle : 0.745 8.842 3017 Z= 0.389 Chirality : 0.046 0.221 309 Planarity : 0.006 0.062 384 Dihedral : 6.054 30.873 301 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.00 % Allowed : 18.88 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.05 (0.52), residues: 120 loop : -1.67 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.002 PHE H 106 TYR 0.015 0.003 TYR H 102 ARG 0.002 0.001 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 65) hydrogen bonds : angle 6.32672 ( 165) SS BOND : bond 0.00455 ( 7) SS BOND : angle 2.52302 ( 14) covalent geometry : bond 0.00484 ( 2216) covalent geometry : angle 0.72706 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.6792 (pt0) cc_final: 0.6512 (mt0) REVERT: L 61 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5906 (mtm180) REVERT: L 81 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7386 (mt-10) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 1.2647 time to fit residues: 45.2844 Evaluate side-chains 33 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.213059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.193374 restraints weight = 2477.529| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.11 r_work: 0.4089 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2223 Z= 0.165 Angle : 0.709 8.326 3017 Z= 0.368 Chirality : 0.044 0.236 309 Planarity : 0.005 0.064 384 Dihedral : 5.888 30.057 301 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.00 % Allowed : 17.60 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.05 (0.52), residues: 120 loop : -1.68 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.005 0.002 HIS L 91 PHE 0.010 0.001 PHE H 106 TYR 0.012 0.002 TYR H 102 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 65) hydrogen bonds : angle 6.11365 ( 165) SS BOND : bond 0.00402 ( 7) SS BOND : angle 2.10582 ( 14) covalent geometry : bond 0.00397 ( 2216) covalent geometry : angle 0.69601 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.6203 (m-80) cc_final: 0.5815 (m-80) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 1.3002 time to fit residues: 46.5478 Evaluate side-chains 33 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1360 CYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 17 optimal weight: 0.0770 overall best weight: 0.3350 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.215332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195654 restraints weight = 2484.359| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.12 r_work: 0.4124 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2223 Z= 0.144 Angle : 0.692 8.795 3017 Z= 0.357 Chirality : 0.044 0.245 309 Planarity : 0.005 0.062 384 Dihedral : 5.750 27.488 301 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.15 % Allowed : 19.31 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.08 (0.52), residues: 121 loop : -1.60 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.005 0.001 HIS L 91 PHE 0.008 0.001 PHE H 106 TYR 0.011 0.002 TYR H 94 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 65) hydrogen bonds : angle 5.95995 ( 165) SS BOND : bond 0.00359 ( 7) SS BOND : angle 1.78764 ( 14) covalent geometry : bond 0.00348 ( 2216) covalent geometry : angle 0.68229 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: H 39 GLN cc_start: 0.6730 (pt0) cc_final: 0.6315 (mt0) REVERT: H 80 TYR cc_start: 0.6134 (m-80) cc_final: 0.5797 (m-80) REVERT: L 81 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7294 (mt-10) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 1.1356 time to fit residues: 38.5075 Evaluate side-chains 34 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1360 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.212269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.192482 restraints weight = 2519.404| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.12 r_work: 0.4079 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2223 Z= 0.184 Angle : 0.729 8.417 3017 Z= 0.379 Chirality : 0.045 0.231 309 Planarity : 0.006 0.065 384 Dihedral : 5.995 28.534 301 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.58 % Allowed : 19.31 % Favored : 78.11 % 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: -1.45 (0.52), residues: 270 helix: None (None), residues: 0 sheet: -0.12 (0.52), residues: 120 loop : -1.73 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.005 0.002 HIS L 91 PHE 0.011 0.001 PHE H 106 TYR 0.014 0.002 TYR H 102 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 65) hydrogen bonds : angle 6.30357 ( 165) SS BOND : bond 0.00433 ( 7) SS BOND : angle 2.17207 ( 14) covalent geometry : bond 0.00439 ( 2216) covalent geometry : angle 0.71592 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.25 seconds wall clock time: 41 minutes 30.98 seconds (2490.98 seconds total)