Starting phenix.real_space_refine on Sun Mar 10 14:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_36406.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_36406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_36406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_36406.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlw_36406/03_2024/8jlw_36406.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.64, per 1000 atoms: 0.76 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 405.9 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: 0.28 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: 0.54 Time building geometry restraints manager: 0.91 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: 100.44 - 107.15: 81 107.15 - 113.86: 1173 113.86 - 120.57: 808 120.57 - 127.28: 906 127.28 - 133.99: 35 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 2.440 nonbonded pdb=" O PRO H 7 " pdb=" OG1 THR H 113 " model vdw 2.273 2.440 nonbonded pdb=" ND2 ASN A1194 " pdb=" O CYS A1198 " model vdw 2.316 2.520 nonbonded pdb=" ND2 ASN H 55 " pdb=" OD2 ASP H 57 " model vdw 2.321 2.520 nonbonded pdb=" O TRP H 47 " pdb=" ND2 ASN H 61 " model vdw 2.335 2.520 ... (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 ========== 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: 2.340 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: 11.400 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.060 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- 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 2216 Z= 0.295 Angle : 0.694 7.315 3003 Z= 0.373 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 *********************** 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 fitting. 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: 1.1305 time to fit residues: 49.7668 Evaluate side-chains 34 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2216 Z= 0.324 Angle : 0.703 8.761 3003 Z= 0.373 Chirality : 0.044 0.203 309 Planarity : 0.005 0.053 384 Dihedral : 6.391 23.742 301 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.29 % Allowed : 12.02 % Favored : 86.70 % 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: -1.50 (0.52), residues: 270 helix: None (None), residues: 0 sheet: -0.40 (0.51), residues: 120 loop : -1.52 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.006 0.002 HIS L 91 PHE 0.011 0.002 PHE H 29 TYR 0.017 0.003 TYR A1358 ARG 0.002 0.000 ARG A1189 *********************** 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 42 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.249 Fit side-chains REVERT: H 39 GLN cc_start: 0.7188 (pt0) cc_final: 0.6649 (tt0) REVERT: L 81 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6695 (mt-10) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 1.0060 time to fit residues: 43.3996 Evaluate side-chains 39 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER 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 6 optimal weight: 0.0370 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2216 Z= 0.243 Angle : 0.641 6.654 3003 Z= 0.337 Chirality : 0.043 0.230 309 Planarity : 0.005 0.053 384 Dihedral : 6.060 22.584 301 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.58 % Allowed : 15.88 % Favored : 81.55 % 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: -1.45 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.36 (0.52), residues: 120 loop : -1.49 (0.50), 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 0.007 0.001 PHE L 98 TYR 0.012 0.002 TYR H 102 ARG 0.002 0.000 ARG A1189 *********************** 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 43 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.238 Fit side-chains REVERT: H 39 GLN cc_start: 0.7184 (pt0) cc_final: 0.6783 (tt0) REVERT: H 80 TYR cc_start: 0.5594 (m-80) cc_final: 0.5273 (m-80) REVERT: L 81 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7307 (mm-30) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 1.0638 time to fit residues: 44.7249 Evaluate side-chains 40 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2216 Z= 0.272 Angle : 0.661 7.408 3003 Z= 0.350 Chirality : 0.043 0.216 309 Planarity : 0.005 0.057 384 Dihedral : 6.095 22.125 301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.72 % Allowed : 16.74 % 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: -1.47 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.39 (0.52), residues: 120 loop : -1.49 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.006 0.002 HIS L 91 PHE 0.008 0.001 PHE L 98 TYR 0.014 0.002 TYR H 102 ARG 0.001 0.000 ARG A1189 *********************** 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 46 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.248 Fit side-chains REVERT: H 39 GLN cc_start: 0.7102 (pt0) cc_final: 0.6785 (tt0) REVERT: L 81 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7277 (mm-30) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 1.0579 time to fit residues: 44.5287 Evaluate side-chains 40 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 18 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2216 Z= 0.255 Angle : 0.655 7.427 3003 Z= 0.345 Chirality : 0.043 0.226 309 Planarity : 0.005 0.059 384 Dihedral : 5.994 21.202 301 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.29 % Allowed : 16.74 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.31 (0.52), residues: 118 loop : -1.42 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.005 0.002 HIS L 91 PHE 0.007 0.001 PHE L 98 TYR 0.014 0.002 TYR H 95 ARG 0.001 0.000 ARG A1189 *********************** 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 47 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.251 Fit side-chains REVERT: H 39 GLN cc_start: 0.7052 (pt0) cc_final: 0.6780 (tt0) REVERT: L 81 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7226 (mm-30) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.9795 time to fit residues: 45.2661 Evaluate side-chains 42 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 18 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2216 Z= 0.287 Angle : 0.691 7.824 3003 Z= 0.362 Chirality : 0.043 0.208 309 Planarity : 0.005 0.064 384 Dihedral : 6.167 20.845 301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.86 % Allowed : 18.03 % 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: -1.39 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.32 (0.53), residues: 118 loop : -1.44 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.006 0.002 HIS L 91 PHE 0.008 0.001 PHE H 106 TYR 0.014 0.003 TYR A1358 ARG 0.001 0.000 ARG A1189 *********************** 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 46 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.237 Fit side-chains REVERT: A 1359 TYR cc_start: 0.6941 (p90) cc_final: 0.6741 (p90) REVERT: H 39 GLN cc_start: 0.7177 (pt0) cc_final: 0.6831 (tt0) REVERT: L 81 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7233 (mm-30) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.9973 time to fit residues: 44.0354 Evaluate side-chains 42 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 18 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2216 Z= 0.305 Angle : 0.699 7.709 3003 Z= 0.367 Chirality : 0.044 0.210 309 Planarity : 0.006 0.067 384 Dihedral : 6.251 20.925 301 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.86 % Allowed : 19.31 % Favored : 76.82 % 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: -1.48 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.44 (0.53), residues: 120 loop : -1.44 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.006 0.002 HIS L 91 PHE 0.009 0.002 PHE L 98 TYR 0.015 0.003 TYR A1358 ARG 0.002 0.001 ARG L 24 *********************** 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 46 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.225 Fit side-chains REVERT: H 39 GLN cc_start: 0.7284 (pt0) cc_final: 0.6841 (tt0) REVERT: L 81 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6894 (mt-10) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.9778 time to fit residues: 44.1992 Evaluate side-chains 43 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 18 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2216 Z= 0.259 Angle : 0.680 7.314 3003 Z= 0.355 Chirality : 0.043 0.220 309 Planarity : 0.005 0.065 384 Dihedral : 6.045 20.735 301 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.43 % Allowed : 19.74 % Favored : 76.82 % 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: -1.43 (0.53), residues: 270 helix: None (None), residues: 0 sheet: -0.37 (0.53), residues: 119 loop : -1.44 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.006 0.002 HIS L 91 PHE 0.007 0.001 PHE L 98 TYR 0.015 0.002 TYR H 95 ARG 0.001 0.000 ARG A1189 *********************** 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 43 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.235 Fit side-chains REVERT: A 1359 TYR cc_start: 0.6946 (p90) cc_final: 0.6677 (p90) REVERT: H 39 GLN cc_start: 0.7215 (pt0) cc_final: 0.6851 (tt0) REVERT: L 81 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7210 (mm-30) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 1.0132 time to fit residues: 42.6505 Evaluate side-chains 41 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 18 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2216 Z= 0.154 Angle : 0.603 7.011 3003 Z= 0.308 Chirality : 0.041 0.237 309 Planarity : 0.005 0.057 384 Dihedral : 5.228 20.049 301 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.58 % Allowed : 20.60 % Favored : 76.82 % 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: -1.37 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.39 (0.52), residues: 123 loop : -1.35 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.004 0.001 HIS L 91 PHE 0.005 0.001 PHE L 71 TYR 0.010 0.001 TYR H 105 ARG 0.001 0.000 ARG L 24 *********************** 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 46 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.265 Fit side-chains REVERT: A 1359 TYR cc_start: 0.6825 (p90) cc_final: 0.6580 (p90) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 1.0882 time to fit residues: 48.0011 Evaluate side-chains 37 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.0040 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2216 Z= 0.208 Angle : 0.641 7.261 3003 Z= 0.331 Chirality : 0.042 0.224 309 Planarity : 0.005 0.059 384 Dihedral : 5.461 19.608 301 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.15 % Allowed : 21.89 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.37 (0.53), residues: 123 loop : -1.25 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.004 0.001 HIS L 91 PHE 0.008 0.001 PHE H 106 TYR 0.011 0.002 TYR H 102 ARG 0.001 0.000 ARG L 61 ********************** 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 41 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.241 Fit side-chains REVERT: A 1359 TYR cc_start: 0.6918 (p90) cc_final: 0.6660 (p90) outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 1.0196 time to fit residues: 40.9022 Evaluate side-chains 38 residues out of total 233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.208284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188869 restraints weight = 2430.343| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.01 r_work: 0.4052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2216 Z= 0.272 Angle : 0.683 7.304 3003 Z= 0.355 Chirality : 0.042 0.213 309 Planarity : 0.006 0.064 384 Dihedral : 5.770 20.081 301 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.15 % Allowed : 21.89 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.54), residues: 270 helix: None (None), residues: 0 sheet: -0.24 (0.53), residues: 121 loop : -1.22 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1197 HIS 0.005 0.002 HIS L 91 PHE 0.007 0.001 PHE L 98 TYR 0.014 0.002 TYR H 94 ARG 0.001 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.76 seconds wall clock time: 29 minutes 31.22 seconds (1771.22 seconds total)