Starting phenix.real_space_refine on Wed Mar 5 15:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2025/7rzu_24778.cif" } resolution = 2.3 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= 0.020 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 1500 2.51 5 N 426 2.21 5 O 513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Restraints were copied for chains: D, F, C, B Time building chain proxies: 1.87, per 1000 atoms: 0.77 Number of scatterers: 2439 At special positions: 0 Unit cell: (44.8938, 51.4238, 116.724, 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 513 8.00 N 426 7.00 C 1500 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: 0.63 Conformation dependent library (CDL) restraints added in 307.3 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 removed outlier: 3.521A pdb=" N GLU A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 988 removed outlier: 3.522A pdb=" N GLU B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 988 removed outlier: 3.521A pdb=" N GLU C 988 " --> pdb=" O LEU C 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.675A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.676A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.676A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 229 hydrogen bonds defined for protein. 687 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: 0.67 Time building geometry restraints manager: 0.74 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: 465 1.29 - 1.35: 399 1.35 - 1.42: 48 1.42 - 1.48: 366 1.48 - 1.54: 1161 Bond restraints: 2439 Sorted by residual: bond pdb=" N ILE D1179 " pdb=" CA ILE D1179 " ideal model delta sigma weight residual 1.459 1.449 0.010 1.25e-02 6.40e+03 6.75e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.73e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.49e-01 bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.41e-01 bond pdb=" N ILE E1179 " pdb=" CA ILE E1179 " ideal model delta sigma weight residual 1.459 1.449 0.010 1.25e-02 6.40e+03 5.93e-01 ... (remaining 2434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 3235 1.47 - 2.94: 41 2.94 - 4.41: 9 4.41 - 5.88: 0 5.88 - 7.36: 3 Bond angle restraints: 3288 Sorted by residual: angle pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sigma weight residual 116.30 123.66 -7.36 3.50e+00 8.16e-02 4.42e+00 angle pdb=" CA LEU B 984 " pdb=" CB LEU B 984 " pdb=" CG LEU B 984 " ideal model delta sigma weight residual 116.30 123.65 -7.35 3.50e+00 8.16e-02 4.40e+00 angle pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sigma weight residual 116.30 123.64 -7.34 3.50e+00 8.16e-02 4.40e+00 angle pdb=" C SER B 982 " pdb=" N ARG B 983 " pdb=" CA ARG B 983 " ideal model delta sigma weight residual 120.44 117.62 2.82 1.36e+00 5.41e-01 4.31e+00 angle pdb=" C SER C 982 " pdb=" N ARG C 983 " pdb=" CA ARG C 983 " ideal model delta sigma weight residual 120.44 117.62 2.82 1.36e+00 5.41e-01 4.31e+00 ... (remaining 3283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1413 17.83 - 35.65: 96 35.65 - 53.48: 9 53.48 - 71.30: 9 71.30 - 89.13: 3 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" CA ARG B 983 " pdb=" C ARG B 983 " pdb=" N LEU B 984 " pdb=" CA LEU B 984 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 983 " pdb=" C ARG A 983 " pdb=" N LEU A 984 " pdb=" CA LEU A 984 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG C 983 " pdb=" C ARG C 983 " pdb=" N LEU C 984 " pdb=" CA LEU C 984 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 332 0.042 - 0.084: 73 0.084 - 0.125: 9 0.125 - 0.167: 0 0.167 - 0.209: 3 Chirality restraints: 417 Sorted by residual: chirality pdb=" CG LEU A 984 " pdb=" CB LEU A 984 " pdb=" CD1 LEU A 984 " pdb=" CD2 LEU A 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU B 984 " pdb=" CB LEU B 984 " pdb=" CD1 LEU B 984 " pdb=" CD2 LEU B 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU C 984 " pdb=" CB LEU C 984 " pdb=" CD1 LEU C 984 " pdb=" CD2 LEU C 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 414 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 983 " -0.196 9.50e-02 1.11e+02 8.78e-02 4.80e+00 pdb=" NE ARG C 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 983 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 983 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.194 9.50e-02 1.11e+02 8.72e-02 4.73e+00 pdb=" NE ARG B 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.194 9.50e-02 1.11e+02 8.71e-02 4.72e+00 pdb=" NE ARG A 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.005 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 423 2.75 - 3.29: 2544 3.29 - 3.82: 4286 3.82 - 4.36: 4758 4.36 - 4.90: 8146 Nonbonded interactions: 20157 Sorted by model distance: nonbonded pdb=" O LEU A 984 " pdb=" NH2 ARG B 983 " model vdw 2.212 3.120 nonbonded pdb=" O LEU B 984 " pdb=" NH2 ARG C 983 " model vdw 2.214 3.120 nonbonded pdb=" NH2 ARG A 983 " pdb=" O LEU C 984 " model vdw 2.234 3.120 nonbonded pdb=" NE2 GLN C 965 " pdb=" O ASP E1168 " model vdw 2.316 3.120 nonbonded pdb=" NE2 GLN B 965 " pdb=" O ASP D1168 " model vdw 2.334 3.120 ... (remaining 20152 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 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.680 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.006 0.023 2439 Z= 0.381 Angle : 0.505 7.356 3288 Z= 0.280 Chirality : 0.039 0.209 417 Planarity : 0.008 0.088 432 Dihedral : 13.614 89.129 912 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 1.69 (0.45), residues: 312 helix: 1.78 (0.30), residues: 246 sheet: None (None), residues: 0 loop : -1.39 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE C 970 ARG 0.005 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 974 SER cc_start: 0.8337 (p) cc_final: 0.7704 (p) REVERT: F 1173 ASN cc_start: 0.8702 (t0) cc_final: 0.8464 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.6877 time to fit residues: 25.9449 Evaluate side-chains 35 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN C 935 GLN D1173 ASN E1194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.142129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.124295 restraints weight = 3296.398| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.08 r_work: 0.4009 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2439 Z= 0.195 Angle : 0.461 8.949 3288 Z= 0.223 Chirality : 0.034 0.141 417 Planarity : 0.002 0.020 432 Dihedral : 3.334 12.843 324 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.70 % Allowed : 7.02 % Favored : 92.28 % 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: 4.30 (0.46), residues: 312 helix: 3.67 (0.29), residues: 243 sheet: None (None), residues: 0 loop : -0.50 (0.83), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 970 ARG 0.003 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1173 ASN cc_start: 0.8847 (t0) cc_final: 0.8644 (t0) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.7531 time to fit residues: 25.1964 Evaluate side-chains 31 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.141949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.125679 restraints weight = 3250.450| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.95 r_work: 0.4035 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2439 Z= 0.148 Angle : 0.448 10.153 3288 Z= 0.205 Chirality : 0.032 0.108 417 Planarity : 0.002 0.021 432 Dihedral : 2.985 9.637 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.11 % Allowed : 5.96 % Favored : 91.93 % 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: 5.22 (0.44), residues: 312 helix: 4.34 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.22 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE B 970 ARG 0.004 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8555 (mt) cc_final: 0.8343 (mt) REVERT: F 1173 ASN cc_start: 0.8798 (t0) cc_final: 0.8594 (t0) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.7332 time to fit residues: 26.0903 Evaluate side-chains 35 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.124946 restraints weight = 3260.212| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.97 r_work: 0.3957 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2439 Z= 0.189 Angle : 0.409 9.048 3288 Z= 0.197 Chirality : 0.032 0.106 417 Planarity : 0.002 0.016 432 Dihedral : 2.969 8.657 324 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.46 % Allowed : 7.02 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.35 (0.44), residues: 312 helix: 4.43 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 970 ARG 0.003 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 984 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8072 (pp) REVERT: B 973 ILE cc_start: 0.8620 (mt) cc_final: 0.8385 (mt) REVERT: F 1173 ASN cc_start: 0.8878 (t0) cc_final: 0.8663 (t0) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.7007 time to fit residues: 25.7008 Evaluate side-chains 36 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.149465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.134666 restraints weight = 3310.719| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.91 r_work: 0.4015 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2439 Z= 0.244 Angle : 0.450 8.849 3288 Z= 0.216 Chirality : 0.034 0.107 417 Planarity : 0.003 0.054 432 Dihedral : 3.110 8.890 324 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.51 % Allowed : 7.37 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.20 (0.44), residues: 312 helix: 4.24 (0.28), residues: 246 sheet: None (None), residues: 0 loop : -0.11 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.008 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 984 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7838 (pp) REVERT: B 973 ILE cc_start: 0.8618 (mt) cc_final: 0.8399 (mt) outliers start: 10 outliers final: 4 residues processed: 34 average time/residue: 0.5993 time to fit residues: 21.4461 Evaluate side-chains 35 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 965 GLN D1173 ASN F1173 ASN F1194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.135485 restraints weight = 3294.136| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.89 r_work: 0.3987 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2439 Z= 0.181 Angle : 0.465 9.966 3288 Z= 0.222 Chirality : 0.032 0.106 417 Planarity : 0.002 0.018 432 Dihedral : 3.015 10.179 324 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.86 % Allowed : 7.37 % Favored : 88.77 % 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: 5.34 (0.44), residues: 312 helix: 4.31 (0.27), residues: 246 sheet: None (None), residues: 0 loop : 0.08 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 970 ARG 0.005 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 984 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8307 (pp) REVERT: B 973 ILE cc_start: 0.8661 (mt) cc_final: 0.8425 (mt) REVERT: F 1173 ASN cc_start: 0.8869 (t0) cc_final: 0.8621 (t0) outliers start: 11 outliers final: 4 residues processed: 35 average time/residue: 0.6025 time to fit residues: 22.2136 Evaluate side-chains 37 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 935 GLN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.150038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.135205 restraints weight = 3343.415| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.92 r_work: 0.4030 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2439 Z= 0.185 Angle : 0.487 10.831 3288 Z= 0.230 Chirality : 0.033 0.107 417 Planarity : 0.002 0.010 432 Dihedral : 3.063 10.320 324 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 8.77 % Favored : 88.07 % 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: 5.14 (0.44), residues: 312 helix: 4.24 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.09 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 970 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8631 (mt) cc_final: 0.8399 (mt) outliers start: 9 outliers final: 4 residues processed: 36 average time/residue: 0.5895 time to fit residues: 22.3529 Evaluate side-chains 36 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN D1173 ASN F1173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.150743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.135971 restraints weight = 3390.835| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.96 r_work: 0.4041 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2439 Z= 0.146 Angle : 0.473 9.984 3288 Z= 0.230 Chirality : 0.033 0.113 417 Planarity : 0.002 0.016 432 Dihedral : 3.014 12.754 324 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.46 % Allowed : 10.88 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.34 (0.45), residues: 312 helix: 4.37 (0.28), residues: 243 sheet: None (None), residues: 0 loop : 0.03 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8607 (mt) cc_final: 0.8387 (mt) REVERT: F 1173 ASN cc_start: 0.8806 (t0) cc_final: 0.8575 (t0) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.6276 time to fit residues: 23.1924 Evaluate side-chains 35 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN D1173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.149951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.134919 restraints weight = 3370.209| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.96 r_work: 0.3986 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2439 Z= 0.181 Angle : 0.500 10.192 3288 Z= 0.241 Chirality : 0.034 0.108 417 Planarity : 0.002 0.016 432 Dihedral : 3.117 12.066 324 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.75 % Allowed : 12.28 % Favored : 85.96 % 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: 5.26 (0.44), residues: 312 helix: 4.31 (0.28), residues: 243 sheet: None (None), residues: 0 loop : 0.04 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE A 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8727 (mt) cc_final: 0.8472 (mt) REVERT: F 1173 ASN cc_start: 0.8855 (t0) cc_final: 0.8623 (t0) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.5187 time to fit residues: 17.6997 Evaluate side-chains 33 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.150280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.135477 restraints weight = 3332.888| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.92 r_work: 0.4035 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2439 Z= 0.210 Angle : 0.495 8.846 3288 Z= 0.240 Chirality : 0.034 0.107 417 Planarity : 0.002 0.016 432 Dihedral : 3.142 11.083 324 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.11 % Allowed : 11.93 % Favored : 85.96 % 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: 5.18 (0.44), residues: 312 helix: 4.25 (0.28), residues: 243 sheet: None (None), residues: 0 loop : 0.01 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 970 ARG 0.001 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8704 (mt) cc_final: 0.8434 (mt) REVERT: F 1173 ASN cc_start: 0.8812 (t0) cc_final: 0.8608 (t0) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.5311 time to fit residues: 18.0782 Evaluate side-chains 34 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.142070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.124228 restraints weight = 3378.722| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.13 r_work: 0.4015 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2439 Z= 0.164 Angle : 0.475 8.437 3288 Z= 0.227 Chirality : 0.033 0.107 417 Planarity : 0.002 0.015 432 Dihedral : 3.006 10.716 324 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.05 % Allowed : 13.33 % Favored : 85.61 % 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: 312 helix: 4.43 (0.27), residues: 243 sheet: None (None), residues: 0 loop : 0.02 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.001 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.87 seconds wall clock time: 40 minutes 3.65 seconds (2403.65 seconds total)