Starting phenix.real_space_refine on Tue Mar 3 11:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_24778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_24778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_24778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_24778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzu_24778/03_2026/7rzu_24778.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: "D" 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: B, C, E, F Time building chain proxies: 0.52, per 1000 atoms: 0.21 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: 0.21 Conformation dependent library (CDL) restraints added in 99.5 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: 0.06 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: 0.38 Time building geometry restraints manager: 0.29 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- 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= 0.276 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG C 983 PHE 0.010 0.002 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 2439) covalent geometry : angle 0.50489 ( 3288) hydrogen bonds : bond 0.03996 ( 229) hydrogen bonds : angle 3.87208 ( 687) *********************** 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 : 0.077 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: 0.2889 time to fit residues: 10.8064 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 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 = 0.142390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.124518 restraints weight = 3321.271| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.08 r_work: 0.3954 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2439 Z= 0.134 Angle : 0.459 8.818 3288 Z= 0.222 Chirality : 0.034 0.142 417 Planarity : 0.002 0.021 432 Dihedral : 3.322 12.868 324 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.70 % Allowed : 7.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.46), residues: 312 helix: 3.71 (0.29), residues: 243 sheet: None (None), residues: 0 loop : -0.49 (0.83), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 983 PHE 0.005 0.001 PHE A 970 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2439) covalent geometry : angle 0.45907 ( 3288) hydrogen bonds : bond 0.03563 ( 229) hydrogen bonds : angle 2.96762 ( 687) *********************** 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 : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1173 ASN cc_start: 0.8883 (t0) cc_final: 0.8672 (t0) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.2806 time to fit residues: 9.3379 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 : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN D1173 ASN E1194 ASN 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 = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.135917 restraints weight = 3289.325| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.91 r_work: 0.4034 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2006 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= 0.122 Angle : 0.445 9.890 3288 Z= 0.206 Chirality : 0.033 0.111 417 Planarity : 0.002 0.023 432 Dihedral : 3.020 9.757 324 Min Nonbonded Distance : 2.613 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.27 (0.44), residues: 312 helix: 4.31 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.15 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 983 PHE 0.003 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2439) covalent geometry : angle 0.44515 ( 3288) hydrogen bonds : bond 0.03429 ( 229) hydrogen bonds : angle 2.74517 ( 687) *********************** 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 : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8524 (mt) cc_final: 0.8315 (mt) outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.2933 time to fit residues: 10.4043 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 : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 D1173 ASN F1194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.140652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.122836 restraints weight = 3350.363| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.10 r_work: 0.3989 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2439 Z= 0.166 Angle : 0.418 8.942 3288 Z= 0.206 Chirality : 0.033 0.105 417 Planarity : 0.002 0.019 432 Dihedral : 3.045 8.763 324 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 7.02 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.12 (0.44), residues: 312 helix: 4.25 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.21 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 983 PHE 0.006 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2439) covalent geometry : angle 0.41813 ( 3288) hydrogen bonds : bond 0.03457 ( 229) hydrogen bonds : angle 2.75089 ( 687) *********************** 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 41 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8674 (mt) cc_final: 0.8447 (mt) outliers start: 8 outliers final: 3 residues processed: 36 average time/residue: 0.3100 time to fit residues: 11.6027 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 968 SER 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 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN B 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 = 0.4377 r_free = 0.4377 target = 0.150906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.136000 restraints weight = 3270.517| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.91 r_work: 0.3969 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2337 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= 0.122 Angle : 0.428 9.256 3288 Z= 0.198 Chirality : 0.032 0.106 417 Planarity : 0.002 0.010 432 Dihedral : 2.893 8.506 324 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.46 % Allowed : 8.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.36 (0.43), residues: 312 helix: 4.46 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.29 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 983 PHE 0.005 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2439) covalent geometry : angle 0.42810 ( 3288) hydrogen bonds : bond 0.03335 ( 229) hydrogen bonds : angle 2.65817 ( 687) *********************** 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 39 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (pp) REVERT: B 973 ILE cc_start: 0.8636 (mt) cc_final: 0.8400 (mt) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.3515 time to fit residues: 12.4201 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 : 0.055 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.140003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.122909 restraints weight = 3270.325| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.09 r_work: 0.4003 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2379 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= 0.159 Angle : 0.437 8.156 3288 Z= 0.213 Chirality : 0.033 0.106 417 Planarity : 0.002 0.010 432 Dihedral : 3.025 8.592 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.86 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.20 (0.44), residues: 312 helix: 4.33 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.27 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 983 PHE 0.005 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2439) covalent geometry : angle 0.43660 ( 3288) hydrogen bonds : bond 0.03414 ( 229) hydrogen bonds : angle 2.73515 ( 687) *********************** 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 41 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: A 973 ILE cc_start: 0.9102 (tp) cc_final: 0.8762 (pp) REVERT: A 984 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8545 (pp) REVERT: B 973 ILE cc_start: 0.8735 (mt) cc_final: 0.8506 (mt) outliers start: 9 outliers final: 4 residues processed: 35 average time/residue: 0.3350 time to fit residues: 12.1700 Evaluate side-chains 38 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 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: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.140784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.123054 restraints weight = 3329.376| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.08 r_work: 0.3992 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2439 Z= 0.172 Angle : 0.446 8.242 3288 Z= 0.218 Chirality : 0.034 0.106 417 Planarity : 0.002 0.011 432 Dihedral : 3.054 8.593 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 9.47 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.04 (0.44), residues: 312 helix: 4.20 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.23 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 983 PHE 0.007 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2439) covalent geometry : angle 0.44565 ( 3288) hydrogen bonds : bond 0.03412 ( 229) hydrogen bonds : angle 2.79513 ( 687) *********************** 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 : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8747 (mt) cc_final: 0.8486 (mt) outliers start: 9 outliers final: 4 residues processed: 34 average time/residue: 0.3219 time to fit residues: 11.4205 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 : 0.096 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4374 r_free = 0.4374 target = 0.150159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.135243 restraints weight = 3355.081| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.91 r_work: 0.3959 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2439 Z= 0.177 Angle : 0.456 9.059 3288 Z= 0.224 Chirality : 0.034 0.107 417 Planarity : 0.002 0.011 432 Dihedral : 3.114 9.299 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 10.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.03 (0.44), residues: 312 helix: 4.18 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.18 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 983 PHE 0.007 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2439) covalent geometry : angle 0.45594 ( 3288) hydrogen bonds : bond 0.03374 ( 229) hydrogen bonds : angle 2.81940 ( 687) *********************** 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 38 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8695 (mt) cc_final: 0.8428 (mt) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.3006 time to fit residues: 10.3667 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 : 0.094 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 977 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 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 22 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.150722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.136055 restraints weight = 3329.249| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.90 r_work: 0.3982 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2439 Z= 0.106 Angle : 0.439 8.873 3288 Z= 0.211 Chirality : 0.032 0.106 417 Planarity : 0.002 0.016 432 Dihedral : 2.918 9.299 324 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.16 % Allowed : 10.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.40 (0.44), residues: 312 helix: 4.44 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.06 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 983 PHE 0.006 0.001 PHE A 970 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 2439) covalent geometry : angle 0.43936 ( 3288) hydrogen bonds : bond 0.03252 ( 229) hydrogen bonds : angle 2.74179 ( 687) *********************** 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 40 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8679 (mt) cc_final: 0.8422 (mt) outliers start: 9 outliers final: 3 residues processed: 33 average time/residue: 0.2993 time to fit residues: 10.3379 Evaluate side-chains 33 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 964 LYS 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 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** 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 = 0.4376 r_free = 0.4376 target = 0.150500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.135652 restraints weight = 3369.549| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.93 r_work: 0.3992 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2637 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= 0.126 Angle : 0.450 9.160 3288 Z= 0.215 Chirality : 0.033 0.107 417 Planarity : 0.002 0.011 432 Dihedral : 2.982 8.646 324 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.40 % Allowed : 11.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.36 (0.44), residues: 312 helix: 4.41 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.06 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 PHE 0.006 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2439) covalent geometry : angle 0.45010 ( 3288) hydrogen bonds : bond 0.03292 ( 229) hydrogen bonds : angle 2.78747 ( 687) ********************** 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 35 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 973 ILE cc_start: 0.8692 (mt) cc_final: 0.8416 (mt) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.3238 time to fit residues: 10.7979 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 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 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.135808 restraints weight = 3370.973| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.93 r_work: 0.4030 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2703 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= 0.131 Angle : 0.456 9.253 3288 Z= 0.217 Chirality : 0.033 0.123 417 Planarity : 0.002 0.011 432 Dihedral : 2.942 8.517 324 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.75 % Allowed : 11.23 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.32 (0.44), residues: 312 helix: 4.39 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.09 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.007 0.001 PHE B 970 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2439) covalent geometry : angle 0.45584 ( 3288) hydrogen bonds : bond 0.03288 ( 229) hydrogen bonds : angle 2.74434 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.82 seconds wall clock time: 18 minutes 49.72 seconds (1129.72 seconds total)