Starting phenix.real_space_refine on Mon Feb 10 20:41:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzr_24775/02_2025/7rzr_24775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzr_24775/02_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_24775/02_2025/7rzr_24775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzr_24775/02_2025/7rzr_24775.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzr_24775/02_2025/7rzr_24775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzr_24775/02_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-5592/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: 1.77, per 1000 atoms: 0.72 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: 0.63 Conformation dependent library (CDL) restraints added in 298.3 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 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: 0.62 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 0.700 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- 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 : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.8176 time to fit residues: 12.1937 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 : 0.248 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.145840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130572 restraints weight = 2931.429| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.77 r_work: 0.3806 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.9398 time to fit residues: 11.9896 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.0470 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 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: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.139431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.123396 restraints weight = 2946.798| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.79 r_work: 0.3819 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2451 Z= 0.194 Angle : 0.282 2.307 3306 Z= 0.166 Chirality : 0.031 0.100 417 Planarity : 0.002 0.017 432 Dihedral : 2.911 9.137 327 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: 5.87 (0.43), residues: 312 helix: 4.77 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.13 (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 0.001 ARG C 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 : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.9249 time to fit residues: 11.8155 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.144597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128928 restraints weight = 2941.336| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.80 r_work: 0.3808 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1485 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= 0.169 Angle : 0.268 2.470 3306 Z= 0.158 Chirality : 0.031 0.102 417 Planarity : 0.002 0.027 432 Dihedral : 2.789 8.936 327 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 : 4.96 % 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: 6.21 (0.43), residues: 312 helix: 5.03 (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 0.003 0.000 PHE C 970 TYR 0.009 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 : 0.218 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.8727 time to fit residues: 12.0110 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.146648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.131213 restraints weight = 2977.835| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.79 r_work: 0.3813 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2451 Z= 0.149 Angle : 0.263 3.068 3306 Z= 0.155 Chirality : 0.031 0.106 417 Planarity : 0.002 0.035 432 Dihedral : 2.725 8.789 327 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.03 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: 6.43 (0.43), residues: 312 helix: 5.17 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.04 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE C 970 TYR 0.008 0.002 TYR C 936 ARG 0.005 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 13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.270 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.8567 time to fit residues: 11.8541 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 : 0.281 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.147565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.132525 restraints weight = 2962.695| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.76 r_work: 0.3815 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2451 Z= 0.183 Angle : 0.283 2.860 3306 Z= 0.165 Chirality : 0.031 0.106 417 Planarity : 0.002 0.033 432 Dihedral : 2.794 8.808 327 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 : 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: 6.31 (0.43), residues: 312 helix: 5.08 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.07 (0.81), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 970 TYR 0.009 0.002 TYR C 936 ARG 0.004 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.263 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.8162 time to fit residues: 12.1828 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 : 0.281 ------------------------------------------------------------------------------- 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: 0.4980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.146758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.131157 restraints weight = 2999.597| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.81 r_work: 0.3809 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2451 Z= 0.157 Angle : 0.274 3.160 3306 Z= 0.159 Chirality : 0.031 0.106 417 Planarity : 0.002 0.027 432 Dihedral : 2.731 8.607 327 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.44 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: 6.47 (0.43), residues: 312 helix: 5.20 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.10 (0.81), 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 0.003 0.000 ARG B 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 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.288 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.7498 time to fit residues: 12.8241 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 : 0.283 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 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 = 0.4224 r_free = 0.4224 target = 0.146166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.130536 restraints weight = 2999.916| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.81 r_work: 0.3805 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2451 Z= 0.227 Angle : 0.299 2.587 3306 Z= 0.176 Chirality : 0.032 0.105 417 Planarity : 0.002 0.022 432 Dihedral : 2.854 9.244 327 Min Nonbonded Distance : 2.630 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: 6.23 (0.43), residues: 312 helix: 5.00 (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 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.213 Fit side-chains REVERT: B 983 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7639 (ttp-170) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.7687 time to fit residues: 12.2364 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 : 0.276 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.137667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120969 restraints weight = 2946.015| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.82 r_work: 0.3800 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1848 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= 0.199 Angle : 0.282 2.660 3306 Z= 0.166 Chirality : 0.032 0.106 417 Planarity : 0.002 0.020 432 Dihedral : 2.802 8.892 327 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.44 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: 6.34 (0.43), residues: 312 helix: 5.08 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.16 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 TYR 0.009 0.002 TYR C 936 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.295 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.9637 time to fit residues: 16.2078 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 : 0.249 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.146038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.131283 restraints weight = 2990.334| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.75 r_work: 0.3808 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1858 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= 0.276 Angle : 0.326 3.888 3306 Z= 0.186 Chirality : 0.033 0.105 417 Planarity : 0.002 0.026 432 Dihedral : 2.951 9.408 327 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 : 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: 6.03 (0.43), residues: 312 helix: 4.85 (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 0.005 0.001 PHE C 970 TYR 0.011 0.002 TYR C 936 ARG 0.003 0.000 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.289 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.8981 time to fit residues: 16.0338 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.145765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.131069 restraints weight = 2985.399| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.75 r_work: 0.3807 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1893 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= 0.276 Angle : 0.317 2.746 3306 Z= 0.183 Chirality : 0.033 0.106 417 Planarity : 0.002 0.028 432 Dihedral : 2.967 9.478 327 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: 5.95 (0.43), residues: 312 helix: 4.79 (0.25), 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 0.004 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1998.80 seconds wall clock time: 36 minutes 11.71 seconds (2171.71 seconds total)