Starting phenix.real_space_refine on Wed Mar 5 15:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzr_24775/03_2025/7rzr_24775.cif" } resolution = 2.27 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= 0.018 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 1515 2.51 5 N 426 2.21 5 O 507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 535 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: 1.75, per 1000 atoms: 0.71 Number of scatterers: 2448 At special positions: 0 Unit cell: (50.6075, 42.445, 117.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 507 8.00 N 426 7.00 C 1515 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: 0.65 Conformation dependent library (CDL) restraints added in 300.0 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: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 459 1.29 - 1.35: 399 1.35 - 1.41: 71 1.41 - 1.48: 361 1.48 - 1.54: 1161 Bond restraints: 2451 Sorted by residual: bond pdb=" CB ASN A 955 " pdb=" CG ASN A 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.50e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.32e-01 bond pdb=" CB ASN B 955 " pdb=" CG ASN B 955 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.26e-01 bond pdb=" CE1 PHE C 970 " pdb=" CZ PHE C 970 " ideal model delta sigma weight residual 1.382 1.356 0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.35e-01 ... (remaining 2446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.64: 3030 0.64 - 1.27: 225 1.27 - 1.91: 39 1.91 - 2.55: 6 2.55 - 3.18: 6 Bond angle restraints: 3306 Sorted by residual: angle pdb=" CA TYR A 936 " pdb=" CB TYR A 936 " pdb=" CG TYR A 936 " ideal model delta sigma weight residual 113.90 116.03 -2.13 1.80e+00 3.09e-01 1.40e+00 angle pdb=" CA TYR C 936 " pdb=" CB TYR C 936 " pdb=" CG TYR C 936 " ideal model delta sigma weight residual 113.90 116.00 -2.10 1.80e+00 3.09e-01 1.36e+00 angle pdb=" CA TYR B 936 " pdb=" CB TYR B 936 " pdb=" CG TYR B 936 " ideal model delta sigma weight residual 113.90 115.96 -2.06 1.80e+00 3.09e-01 1.32e+00 angle pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " pdb=" CD2 LEU C 984 " ideal model delta sigma weight residual 110.70 113.75 -3.05 3.00e+00 1.11e-01 1.03e+00 angle pdb=" CB LEU B 984 " pdb=" CG LEU B 984 " pdb=" CD2 LEU B 984 " ideal model delta sigma weight residual 110.70 113.75 -3.05 3.00e+00 1.11e-01 1.03e+00 ... (remaining 3301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1404 17.88 - 35.77: 102 35.77 - 53.65: 9 53.65 - 71.53: 9 71.53 - 89.42: 6 Dihedral angle restraints: 1530 sinusoidal: 591 harmonic: 939 Sorted by residual: dihedral pdb=" CB GLU C 918 " pdb=" CG GLU C 918 " pdb=" CD GLU C 918 " pdb=" OE1 GLU C 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.57 -63.57 1 3.00e+01 1.11e-03 5.92e+00 dihedral pdb=" CB GLU B 918 " pdb=" CG GLU B 918 " pdb=" CD GLU B 918 " pdb=" OE1 GLU B 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.51 -63.51 1 3.00e+01 1.11e-03 5.91e+00 dihedral pdb=" CB GLU A 918 " pdb=" CG GLU A 918 " pdb=" CD GLU A 918 " pdb=" OE1 GLU A 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.51 -63.51 1 3.00e+01 1.11e-03 5.91e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 188 0.024 - 0.048: 173 0.048 - 0.072: 41 0.072 - 0.096: 9 0.096 - 0.120: 6 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA PHE C 970 " pdb=" N PHE C 970 " pdb=" C PHE C 970 " pdb=" CB PHE C 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA PHE A 970 " pdb=" N PHE A 970 " pdb=" C PHE A 970 " pdb=" CB PHE A 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA PHE B 970 " pdb=" N PHE B 970 " pdb=" C PHE B 970 " pdb=" CB PHE B 970 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 414 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 936 " 0.007 2.00e-02 2.50e+03 5.85e-03 6.84e-01 pdb=" CG TYR B 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 936 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 936 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 936 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 936 " 0.007 2.00e-02 2.50e+03 5.75e-03 6.61e-01 pdb=" CG TYR C 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 936 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 936 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 936 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 936 " 0.006 2.00e-02 2.50e+03 5.53e-03 6.13e-01 pdb=" CG TYR A 936 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 936 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 936 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 936 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 936 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 936 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 936 " 0.000 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 968 2.93 - 3.42: 2824 3.42 - 3.91: 4147 3.91 - 4.41: 4468 4.41 - 4.90: 7504 Nonbonded interactions: 19911 Sorted by model distance: nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.436 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.438 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.443 3.120 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASN D1173 " pdb=" N ALA D1174 " model vdw 2.508 3.120 ... (remaining 19906 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.007 0.027 2451 Z= 0.434 Angle : 0.400 3.183 3306 Z= 0.230 Chirality : 0.035 0.120 417 Planarity : 0.002 0.007 432 Dihedral : 14.340 89.418 912 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.41), residues: 312 helix: 2.38 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.25 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE A 970 TYR 0.014 0.004 TYR B 936 ARG 0.001 0.000 ARG A 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 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.7852 time to fit residues: 11.7388 Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 8 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: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.145210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.129973 restraints weight = 2933.785| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.78 r_work: 0.3805 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2451 Z= 0.237 Angle : 0.311 2.432 3306 Z= 0.181 Chirality : 0.032 0.099 417 Planarity : 0.002 0.014 432 Dihedral : 3.114 9.562 327 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 5.02 (0.43), residues: 312 helix: 4.20 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.58 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.013 0.003 TYR C 936 ARG 0.003 0.000 ARG C 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 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.9616 time to fit residues: 12.2518 Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.148551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.133401 restraints weight = 2954.686| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.76 r_work: 0.3827 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2451 Z= 0.191 Angle : 0.281 2.297 3306 Z= 0.165 Chirality : 0.031 0.100 417 Planarity : 0.002 0.017 432 Dihedral : 2.901 9.131 327 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: 5.89 (0.43), residues: 312 helix: 4.79 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.12 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.011 0.002 TYR C 936 ARG 0.003 0.000 ARG B 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 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.9053 time to fit residues: 11.5506 Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.138957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121366 restraints weight = 2963.011| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.92 r_work: 0.3799 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2451 Z= 0.210 Angle : 0.284 2.411 3306 Z= 0.166 Chirality : 0.032 0.101 417 Planarity : 0.002 0.028 432 Dihedral : 2.880 9.176 327 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % 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: 6.00 (0.43), residues: 312 helix: 4.87 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.10 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 970 TYR 0.011 0.002 TYR C 936 ARG 0.005 0.001 ARG B 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 13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.257 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.9107 time to fit residues: 12.5842 Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 24 optimal weight: 0.0470 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.137561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.120591 restraints weight = 2989.124| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.87 r_work: 0.3795 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2451 Z= 0.159 Angle : 0.266 3.005 3306 Z= 0.157 Chirality : 0.031 0.102 417 Planarity : 0.002 0.036 432 Dihedral : 2.758 8.883 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.96 % Favored : 94.68 % 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: 6.32 (0.43), residues: 312 helix: 5.09 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.03 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 927 TYR 0.008 0.002 TYR C 936 ARG 0.004 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.283 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.9445 time to fit residues: 12.0726 Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.120483 restraints weight = 2964.556| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.86 r_work: 0.3789 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2451 Z= 0.223 Angle : 0.298 2.862 3306 Z= 0.172 Chirality : 0.032 0.101 417 Planarity : 0.002 0.037 432 Dihedral : 2.876 9.104 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 5.67 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.11 (0.43), residues: 312 helix: 4.92 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.08 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.010 0.002 TYR C 936 ARG 0.004 0.001 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 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.279 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.7931 time to fit residues: 12.6951 Evaluate side-chains 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.147449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.132380 restraints weight = 3010.934| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.77 r_work: 0.3814 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2451 Z= 0.161 Angle : 0.293 3.850 3306 Z= 0.166 Chirality : 0.031 0.103 417 Planarity : 0.001 0.016 432 Dihedral : 2.779 9.730 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.03 % Favored : 93.62 % 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: 6.37 (0.43), residues: 312 helix: 5.09 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.19 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE B 927 TYR 0.008 0.002 TYR C 936 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 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.230 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.8463 time to fit residues: 13.4595 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.146230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130869 restraints weight = 3010.063| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.78 r_work: 0.3810 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2451 Z= 0.187 Angle : 0.303 3.427 3306 Z= 0.175 Chirality : 0.032 0.102 417 Planarity : 0.002 0.031 432 Dihedral : 2.829 11.203 327 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 6.03 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.32 (0.43), residues: 312 helix: 5.06 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.17 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 970 TYR 0.008 0.002 TYR C 936 ARG 0.006 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.245 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 15 average time/residue: 0.7812 time to fit residues: 12.4662 Evaluate side-chains 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.145925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.130766 restraints weight = 2952.563| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.76 r_work: 0.3811 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2451 Z= 0.168 Angle : 0.317 6.032 3306 Z= 0.180 Chirality : 0.031 0.116 417 Planarity : 0.002 0.027 432 Dihedral : 2.858 15.068 327 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.03 % Favored : 93.62 % 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: 6.35 (0.43), residues: 312 helix: 5.08 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.18 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE B 927 TYR 0.008 0.002 TYR C 936 ARG 0.009 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.278 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.8131 time to fit residues: 12.1590 Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.144945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.129659 restraints weight = 2980.524| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.79 r_work: 0.3807 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2451 Z= 0.230 Angle : 0.327 4.660 3306 Z= 0.186 Chirality : 0.032 0.102 417 Planarity : 0.002 0.037 432 Dihedral : 2.976 14.848 327 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.38 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.09 (0.43), residues: 312 helix: 4.89 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.010 0.002 TYR C 936 ARG 0.006 0.001 ARG B 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 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.305 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.8041 time to fit residues: 12.0551 Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129681 restraints weight = 2968.738| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.77 r_work: 0.3807 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2451 Z= 0.190 Angle : 0.326 4.839 3306 Z= 0.184 Chirality : 0.032 0.104 417 Planarity : 0.002 0.039 432 Dihedral : 2.939 16.807 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % 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: 6.22 (0.43), residues: 312 helix: 4.99 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.16 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 970 TYR 0.008 0.002 TYR C 936 ARG 0.005 0.001 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.12 seconds wall clock time: 35 minutes 18.01 seconds (2118.01 seconds total)