Starting phenix.real_space_refine on Wed Sep 17 03:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzr_24775/09_2025/7rzr_24775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzr_24775/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rzr_24775/09_2025/7rzr_24775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzr_24775/09_2025/7rzr_24775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzr_24775/09_2025/7rzr_24775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzr_24775/09_2025/7rzr_24775.map" } resolution = 2.27 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= 0.018 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: "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: 0.68, per 1000 atoms: 0.28 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: 0.27 Conformation dependent library (CDL) restraints added in 104.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.07 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: 0.42 Time building geometry restraints manager: 0.30 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: 0.01 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: 1.070 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.710 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- 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= 0.305 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 983 TYR 0.014 0.004 TYR B 936 PHE 0.010 0.002 PHE A 970 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 2451) covalent geometry : angle 0.39959 ( 3306) hydrogen bonds : bond 0.07732 ( 235) hydrogen bonds : angle 2.64312 ( 696) *********************** 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 : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.4280 time to fit residues: 6.2856 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 : 0.097 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.139941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.123327 restraints weight = 2947.053| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.83 r_work: 0.3805 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2451 Z= 0.174 Angle : 0.315 2.419 3306 Z= 0.184 Chirality : 0.033 0.099 417 Planarity : 0.002 0.024 432 Dihedral : 3.138 9.690 327 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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 aren not related in a simple way. whole: 4.95 (0.43), residues: 312 helix: 4.16 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.59 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 983 TYR 0.013 0.003 TYR C 936 PHE 0.003 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 2451) covalent geometry : angle 0.31521 ( 3306) hydrogen bonds : bond 0.03231 ( 235) hydrogen bonds : angle 2.40416 ( 696) *********************** 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 11 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.5569 time to fit residues: 6.4143 Evaluate side-chains 11 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.121002 restraints weight = 3021.040| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.88 r_work: 0.3805 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1318 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= 0.137 Angle : 0.275 2.378 3306 Z= 0.163 Chirality : 0.031 0.100 417 Planarity : 0.002 0.021 432 Dihedral : 2.900 9.217 327 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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 aren not related in a simple way. whole: 5.88 (0.43), residues: 312 helix: 4.78 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.11 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 983 TYR 0.011 0.002 TYR C 936 PHE 0.004 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2451) covalent geometry : angle 0.27544 ( 3306) hydrogen bonds : bond 0.03166 ( 235) hydrogen bonds : angle 2.21124 ( 696) *********************** 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 : 0.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.4609 time to fit residues: 5.8687 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 : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.121333 restraints weight = 2981.864| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.92 r_work: 0.3798 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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= 0.148 Angle : 0.288 2.452 3306 Z= 0.168 Chirality : 0.032 0.101 417 Planarity : 0.002 0.026 432 Dihedral : 2.887 9.184 327 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.00 (0.43), residues: 312 helix: 4.87 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.09 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 983 TYR 0.011 0.002 TYR C 936 PHE 0.005 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2451) covalent geometry : angle 0.28815 ( 3306) hydrogen bonds : bond 0.03233 ( 235) hydrogen bonds : angle 2.21763 ( 696) *********************** 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 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.107 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.4569 time to fit residues: 6.7045 Evaluate side-chains 13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.145747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130303 restraints weight = 2952.636| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.78 r_work: 0.3809 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2451 Z= 0.141 Angle : 0.280 2.890 3306 Z= 0.165 Chirality : 0.032 0.101 417 Planarity : 0.002 0.039 432 Dihedral : 2.839 9.079 327 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.11 (0.43), residues: 312 helix: 4.93 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.00 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 983 TYR 0.010 0.002 TYR C 936 PHE 0.004 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2451) covalent geometry : angle 0.28031 ( 3306) hydrogen bonds : bond 0.03205 ( 235) hydrogen bonds : angle 2.22003 ( 696) *********************** 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 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.098 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.3549 time to fit residues: 5.2358 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 : 0.099 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.137573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.120794 restraints weight = 2964.697| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.83 r_work: 0.3795 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2451 Z= 0.135 Angle : 0.288 2.927 3306 Z= 0.167 Chirality : 0.031 0.102 417 Planarity : 0.002 0.034 432 Dihedral : 2.834 9.119 327 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.17 (0.43), residues: 312 helix: 4.96 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.10 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 983 TYR 0.009 0.002 TYR C 936 PHE 0.003 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2451) covalent geometry : angle 0.28770 ( 3306) hydrogen bonds : bond 0.03180 ( 235) hydrogen bonds : angle 2.21056 ( 696) *********************** 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 : 0.099 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.4062 time to fit residues: 6.3994 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 : 0.094 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.146346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130866 restraints weight = 2925.682| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.76 r_work: 0.3811 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2451 Z= 0.155 Angle : 0.305 2.830 3306 Z= 0.175 Chirality : 0.032 0.102 417 Planarity : 0.001 0.014 432 Dihedral : 2.896 9.700 327 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.07 (0.43), residues: 312 helix: 4.88 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 983 TYR 0.010 0.002 TYR C 936 PHE 0.004 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2451) covalent geometry : angle 0.30501 ( 3306) hydrogen bonds : bond 0.03248 ( 235) hydrogen bonds : angle 2.28255 ( 696) *********************** 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 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.079 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.3203 time to fit residues: 5.3900 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 : 0.065 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.145447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.130310 restraints weight = 2974.333| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.77 r_work: 0.3808 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2451 Z= 0.186 Angle : 0.338 4.034 3306 Z= 0.192 Chirality : 0.033 0.102 417 Planarity : 0.002 0.037 432 Dihedral : 2.997 11.017 327 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.89 (0.43), residues: 312 helix: 4.74 (0.26), residues: 246 sheet: None (None), residues: 0 loop : 0.10 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.011 0.002 TYR C 936 PHE 0.005 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2451) covalent geometry : angle 0.33770 ( 3306) hydrogen bonds : bond 0.03340 ( 235) hydrogen bonds : angle 2.38329 ( 696) *********************** 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 : 0.055 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 15 average time/residue: 0.3458 time to fit residues: 5.4068 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 : 0.086 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.145790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.130834 restraints weight = 3061.110| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.81 r_work: 0.3809 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2451 Z= 0.164 Angle : 0.350 5.784 3306 Z= 0.195 Chirality : 0.033 0.107 417 Planarity : 0.002 0.016 432 Dihedral : 2.995 14.336 327 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 : 0.71 % Allowed : 6.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.94 (0.43), residues: 312 helix: 4.77 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 983 TYR 0.010 0.002 TYR C 936 PHE 0.004 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2451) covalent geometry : angle 0.34952 ( 3306) hydrogen bonds : bond 0.03309 ( 235) hydrogen bonds : angle 2.42180 ( 696) *********************** 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 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.082 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 0.3140 time to fit residues: 4.5999 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 : 0.057 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 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 = 0.4221 r_free = 0.4221 target = 0.144852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129592 restraints weight = 3044.678| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.77 r_work: 0.3810 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.004 0.017 2451 Z= 0.162 Angle : 0.376 9.345 3306 Z= 0.210 Chirality : 0.033 0.106 417 Planarity : 0.002 0.021 432 Dihedral : 3.075 18.109 327 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.86 (0.43), residues: 312 helix: 4.71 (0.26), residues: 246 sheet: None (None), residues: 0 loop : 0.15 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.010 0.002 TYR C 936 PHE 0.004 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2451) covalent geometry : angle 0.37612 ( 3306) hydrogen bonds : bond 0.03333 ( 235) hydrogen bonds : angle 2.50841 ( 696) ********************** 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 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.059 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.3144 time to fit residues: 4.9610 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 : 0.057 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.145433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130320 restraints weight = 3008.972| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.77 r_work: 0.3864 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1961 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= 0.126 Angle : 0.310 4.744 3306 Z= 0.178 Chirality : 0.031 0.104 417 Planarity : 0.003 0.044 432 Dihedral : 2.940 16.172 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.83 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.20 (0.43), residues: 312 helix: 4.96 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.17 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.008 0.002 TYR C 936 PHE 0.003 0.000 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2451) covalent geometry : angle 0.31045 ( 3306) hydrogen bonds : bond 0.03205 ( 235) hydrogen bonds : angle 2.37830 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.85 seconds wall clock time: 18 minutes 27.51 seconds (1107.51 seconds total)