Starting phenix.real_space_refine on Wed Mar 5 15:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.map" model { file = "/net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czi_27098/03_2025/8czi_27098.cif" } resolution = 2.22 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= 0.001 sd= 0.019 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: 3 Type Number sf(0) Gaussians C 1566 2.51 5 N 447 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.80, per 1000 atoms: 0.71 Number of scatterers: 2550 At special positions: 0 Unit cell: (45.71, 49.7913, 117.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 537 8.00 N 447 7.00 C 1566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 327.5 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 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: 0.66 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 486 1.29 - 1.35: 420 1.35 - 1.42: 83 1.42 - 1.48: 361 1.48 - 1.54: 1206 Bond restraints: 2556 Sorted by residual: bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 5.84e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 5.77e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.77e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.75e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.449 0.008 1.15e-02 7.56e+03 4.95e-01 ... (remaining 2551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.58: 3212 0.58 - 1.17: 199 1.17 - 1.75: 35 1.75 - 2.33: 1 2.33 - 2.92: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" C ASP F1165 " pdb=" CA ASP F1165 " pdb=" CB ASP F1165 " ideal model delta sigma weight residual 110.19 111.68 -1.49 1.62e+00 3.81e-01 8.49e-01 angle pdb=" C ASP D1165 " pdb=" CA ASP D1165 " pdb=" CB ASP D1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.39e-01 angle pdb=" C ASP E1165 " pdb=" CA ASP E1165 " pdb=" CB ASP E1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.35e-01 angle pdb=" CA PRO D1162 " pdb=" CB PRO D1162 " pdb=" CG PRO D1162 " ideal model delta sigma weight residual 104.50 106.22 -1.72 1.90e+00 2.77e-01 8.19e-01 angle pdb=" CA PRO E1162 " pdb=" CB PRO E1162 " pdb=" CG PRO E1162 " ideal model delta sigma weight residual 104.50 106.21 -1.71 1.90e+00 2.77e-01 8.14e-01 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1461 17.82 - 35.64: 114 35.64 - 53.46: 9 53.46 - 71.28: 9 71.28 - 89.10: 6 Dihedral angle restraints: 1599 sinusoidal: 618 harmonic: 981 Sorted by residual: dihedral pdb=" N ASN D1187 " pdb=" CA ASN D1187 " pdb=" CB ASN D1187 " pdb=" CG ASN D1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.03 37.03 3 1.50e+01 4.44e-03 6.45e+00 dihedral pdb=" N ASN E1187 " pdb=" CA ASN E1187 " pdb=" CB ASN E1187 " pdb=" CG ASN E1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 dihedral pdb=" N ASN F1187 " pdb=" CA ASN F1187 " pdb=" CB ASN F1187 " pdb=" CG ASN F1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 ... (remaining 1596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 214 0.021 - 0.041: 148 0.041 - 0.062: 59 0.062 - 0.083: 2 0.083 - 0.103: 12 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 ... (remaining 432 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D1161 " -0.012 5.00e-02 4.00e+02 1.79e-02 5.13e-01 pdb=" N PRO D1162 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO D1162 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO D1162 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F1161 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO F1162 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO F1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F1162 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E1161 " 0.012 5.00e-02 4.00e+02 1.76e-02 4.97e-01 pdb=" N PRO E1162 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO E1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO E1162 " 0.010 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 903 2.89 - 3.39: 2866 3.39 - 3.89: 4324 3.89 - 4.40: 4612 4.40 - 4.90: 7926 Nonbonded interactions: 20631 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.382 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.383 3.120 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.384 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.396 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.397 3.120 ... (remaining 20626 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.710 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.040 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.004 0.026 2556 Z= 0.276 Angle : 0.333 2.918 3453 Z= 0.199 Chirality : 0.031 0.103 435 Planarity : 0.002 0.018 456 Dihedral : 14.483 89.102 951 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.41), residues: 327 helix: 3.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.285 Fit side-chains REVERT: B 973 ILE cc_start: 0.8582 (mt) cc_final: 0.8253 (mt) REVERT: C 964 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7962 (ttmt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4671 time to fit residues: 14.6372 Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.141829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.125188 restraints weight = 3271.470| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.61 r_work: 0.3802 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2556 Z= 0.209 Angle : 0.320 2.841 3453 Z= 0.183 Chirality : 0.032 0.098 435 Planarity : 0.002 0.016 456 Dihedral : 2.822 8.871 339 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 5.05 % Favored : 94.28 % 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: 4.73 (0.43), residues: 327 helix: 4.47 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -1.39 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG F1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.315 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.3119 time to fit residues: 9.1462 Evaluate side-chains 25 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.140601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.124025 restraints weight = 3314.686| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.62 r_work: 0.3778 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2556 Z= 0.284 Angle : 0.338 3.250 3453 Z= 0.193 Chirality : 0.034 0.102 435 Planarity : 0.002 0.017 456 Dihedral : 2.932 9.663 339 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 5.39 % Favored : 93.27 % 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: 5.04 (0.43), residues: 327 helix: 4.63 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -1.04 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.009 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.266 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.2906 time to fit residues: 9.8090 Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain E residue 1173 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124257 restraints weight = 3305.741| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.59 r_work: 0.3786 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2556 Z= 0.249 Angle : 0.326 2.957 3453 Z= 0.188 Chirality : 0.033 0.102 435 Planarity : 0.002 0.017 456 Dihedral : 2.865 9.695 339 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 7.07 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.20 (0.43), residues: 327 helix: 4.73 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.93 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.300 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.3137 time to fit residues: 9.8780 Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain E residue 1173 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.140920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124364 restraints weight = 3310.941| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.61 r_work: 0.3786 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2556 Z= 0.224 Angle : 0.320 3.375 3453 Z= 0.182 Chirality : 0.033 0.104 435 Planarity : 0.002 0.017 456 Dihedral : 2.798 9.362 339 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 6.40 % Favored : 92.26 % 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: 5.39 (0.43), residues: 327 helix: 4.86 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.83 (0.64), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.286 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.2159 time to fit residues: 7.3442 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.140771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124229 restraints weight = 3322.428| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.61 r_work: 0.3790 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.179 Angle : 0.318 4.110 3453 Z= 0.178 Chirality : 0.032 0.104 435 Planarity : 0.002 0.015 456 Dihedral : 2.696 9.198 339 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.65 (0.43), residues: 327 helix: 5.05 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.74 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.2393 time to fit residues: 8.0543 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.140604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124381 restraints weight = 3386.422| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.60 r_work: 0.3787 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2556 Z= 0.249 Angle : 0.342 3.542 3453 Z= 0.195 Chirality : 0.033 0.121 435 Planarity : 0.002 0.016 456 Dihedral : 2.810 9.540 339 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.07 % Favored : 91.25 % 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: 5.40 (0.43), residues: 327 helix: 4.85 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.74 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.290 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.2948 time to fit residues: 9.3265 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124231 restraints weight = 3324.935| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.59 r_work: 0.3790 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2556 Z= 0.223 Angle : 0.332 3.574 3453 Z= 0.191 Chirality : 0.033 0.114 435 Planarity : 0.002 0.018 456 Dihedral : 2.759 9.381 339 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.43), residues: 327 helix: 4.89 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.68 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.293 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.2122 time to fit residues: 6.9537 Evaluate side-chains 32 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.133254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114214 restraints weight = 3392.259| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.77 r_work: 0.3762 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2556 Z= 0.237 Angle : 0.359 6.170 3453 Z= 0.198 Chirality : 0.033 0.117 435 Planarity : 0.002 0.017 456 Dihedral : 2.791 9.523 339 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.07 % Favored : 91.25 % 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: 5.41 (0.43), residues: 327 helix: 4.84 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.72 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.006 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.310 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2577 time to fit residues: 7.7690 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.133449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.114332 restraints weight = 3376.525| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.77 r_work: 0.3764 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.212 Angle : 0.350 5.719 3453 Z= 0.194 Chirality : 0.033 0.115 435 Planarity : 0.002 0.015 456 Dihedral : 2.747 9.349 339 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.07 % Favored : 91.25 % 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: 5.50 (0.43), residues: 327 helix: 4.91 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.69 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.294 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.2300 time to fit residues: 7.0110 Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain E residue 1173 ASN Chi-restraints excluded: chain F residue 1166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.133172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.114377 restraints weight = 3408.092| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.77 r_work: 0.3767 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2556 Z= 0.204 Angle : 0.343 5.305 3453 Z= 0.192 Chirality : 0.033 0.112 435 Planarity : 0.002 0.015 456 Dihedral : 2.738 9.362 339 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.43), residues: 327 helix: 4.93 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.69 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.80 seconds wall clock time: 39 minutes 39.07 seconds (2379.07 seconds total)