Starting phenix.real_space_refine on Mon Feb 10 20:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzu_24778/02_2025/7rzu_24778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzu_24778/02_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_24778/02_2025/7rzu_24778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzu_24778/02_2025/7rzu_24778.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzu_24778/02_2025/7rzu_24778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzu_24778/02_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-5592/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: 1.59, per 1000 atoms: 0.65 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 322.8 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: 0.18 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: 0.71 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.740 Find NCS groups from input model: 0.060 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- 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 : 0.283 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: 0.6875 time to fit residues: 25.9195 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 : 0.261 ------------------------------------------------------------------------------- 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 = 0.124297 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: 0.3849 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1173 ASN cc_start: 0.8848 (t0) cc_final: 0.8644 (t0) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.7580 time to fit residues: 25.3819 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 : 0.283 ------------------------------------------------------------------------------- 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: 0.2980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.0000 chunk 27 optimal weight: 0.7980 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.151164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.136246 restraints weight = 3261.878| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.89 r_work: 0.4035 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2439 Z= 0.171 Angle : 0.446 9.979 3288 Z= 0.207 Chirality : 0.033 0.113 417 Planarity : 0.002 0.023 432 Dihedral : 3.036 9.777 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.86 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: 5.23 (0.44), residues: 312 helix: 4.27 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.13 (0.81), residues: 66 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 : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8528 (mt) cc_final: 0.8318 (mt) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.7115 time to fit residues: 25.3810 Evaluate side-chains 37 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.150482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.135620 restraints weight = 3279.041| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.90 r_work: 0.4017 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2439 Z= 0.230 Angle : 0.433 10.659 3288 Z= 0.210 Chirality : 0.034 0.106 417 Planarity : 0.004 0.070 432 Dihedral : 3.159 9.320 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.51 % Allowed : 6.67 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.12 (0.44), residues: 312 helix: 4.25 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.17 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.006 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 42 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8618 (mt) cc_final: 0.8395 (mt) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 0.6847 time to fit residues: 25.1244 Evaluate side-chains 40 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 1175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.150517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135715 restraints weight = 3298.106| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.89 r_work: 0.3984 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2439 Z= 0.195 Angle : 0.443 10.168 3288 Z= 0.206 Chirality : 0.033 0.106 417 Planarity : 0.002 0.026 432 Dihedral : 3.006 8.623 324 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 8.07 % 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: 5.23 (0.44), residues: 312 helix: 4.33 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.13 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 970 ARG 0.002 0.000 ARG A 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: 8 poor density : 32 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8495 (pp) REVERT: B 973 ILE cc_start: 0.8660 (mt) cc_final: 0.8425 (mt) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.7093 time to fit residues: 25.9794 Evaluate side-chains 41 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 965 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 1175 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN F1194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.151659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.137233 restraints weight = 3270.725| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.87 r_work: 0.4003 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2439 Z= 0.128 Angle : 0.420 9.489 3288 Z= 0.197 Chirality : 0.031 0.106 417 Planarity : 0.002 0.009 432 Dihedral : 2.789 7.912 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.11 % Allowed : 9.47 % Favored : 88.42 % 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: 5.60 (0.44), residues: 312 helix: 4.61 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.11 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE B 970 ARG 0.002 0.000 ARG C 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 39 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8659 (mt) cc_final: 0.8413 (mt) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.7134 time to fit residues: 26.1858 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C 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: 0.6980 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.142562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.124710 restraints weight = 3384.087| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.12 r_work: 0.3941 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.026 2439 Z= 0.171 Angle : 0.419 9.178 3288 Z= 0.205 Chirality : 0.032 0.114 417 Planarity : 0.002 0.010 432 Dihedral : 2.891 8.435 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 9.12 % Favored : 87.72 % 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 (0.44), residues: 312 helix: 4.54 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.16 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 970 ARG 0.002 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 : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 973 ILE cc_start: 0.8965 (tp) cc_final: 0.8686 (pp) REVERT: B 973 ILE cc_start: 0.8600 (mt) cc_final: 0.8364 (mt) outliers start: 9 outliers final: 4 residues processed: 34 average time/residue: 0.6995 time to fit residues: 24.9123 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 1175 SER 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: 0.7980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 overall best weight: 0.1450 ------------------------------------------------------------------------------- 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 935 GLN 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 = 0.4401 r_free = 0.4401 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.138146 restraints weight = 3366.793| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.93 r_work: 0.4052 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2834 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= 0.110 Angle : 0.414 8.807 3288 Z= 0.199 Chirality : 0.031 0.107 417 Planarity : 0.001 0.010 432 Dihedral : 2.692 9.192 324 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.07 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: 5.87 (0.44), residues: 312 helix: 4.82 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.07 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE A 970 ARG 0.002 0.000 ARG C 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 : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 973 ILE cc_start: 0.9010 (tp) cc_final: 0.8724 (pp) REVERT: B 973 ILE cc_start: 0.8671 (mt) cc_final: 0.8418 (mt) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.5658 time to fit residues: 21.4458 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 1175 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.0010 chunk 27 optimal weight: 0.6980 overall best weight: 0.3964 ------------------------------------------------------------------------------- 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 = 0.4382 r_free = 0.4382 target = 0.142798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124864 restraints weight = 3388.515| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.12 r_work: 0.3967 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2735 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= 0.175 Angle : 0.417 8.034 3288 Z= 0.209 Chirality : 0.033 0.106 417 Planarity : 0.002 0.011 432 Dihedral : 2.872 9.001 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 11.23 % 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: 5.68 (0.44), residues: 312 helix: 4.68 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.14 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE A 970 ARG 0.002 0.000 ARG C 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 39 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 973 ILE cc_start: 0.9039 (tp) cc_final: 0.8669 (pp) REVERT: B 973 ILE cc_start: 0.8735 (mt) cc_final: 0.8417 (mt) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.6226 time to fit residues: 22.3643 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 1175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.130623 restraints weight = 3227.265| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.11 r_work: 0.4061 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2706 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= 0.194 Angle : 0.424 8.170 3288 Z= 0.214 Chirality : 0.033 0.107 417 Planarity : 0.002 0.011 432 Dihedral : 2.941 9.583 324 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.46 % Allowed : 11.58 % 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: 5.50 (0.44), residues: 312 helix: 4.55 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.16 (0.73), 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 ********************** 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 38 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8816 (mt) cc_final: 0.8512 (mt) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.6251 time to fit residues: 21.7644 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 26 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 ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN D1173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.155557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.139486 restraints weight = 3151.623| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.03 r_work: 0.4015 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2439 Z= 0.250 Angle : 0.430 7.728 3288 Z= 0.222 Chirality : 0.034 0.108 417 Planarity : 0.002 0.011 432 Dihedral : 3.058 9.026 324 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 10.88 % Favored : 86.32 % 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: 5.31 (0.44), residues: 312 helix: 4.38 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.13 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE B 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: 2160.56 seconds wall clock time: 38 minutes 53.33 seconds (2333.33 seconds total)