Starting phenix.real_space_refine on Wed Sep 17 03:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzq_24774/09_2025/7rzq_24774.cif" } resolution = 2.09 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= 0.019 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 1491 2.51 5 N 424 2.21 5 O 506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 2421 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 266 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 0.88, per 1000 atoms: 0.36 Number of scatterers: 2421 At special positions: 0 Unit cell: (44.8938, 51.4238, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 506 8.00 N 424 7.00 C 1491 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: 0.18 Conformation dependent library (CDL) restraints added in 140.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 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: 0.41 Time building geometry restraints manager: 0.25 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: 461 1.29 - 1.35: 397 1.35 - 1.42: 53 1.42 - 1.48: 358 1.48 - 1.54: 1152 Bond restraints: 2421 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.98e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.29e-01 bond pdb=" CA ASN E1178 " pdb=" CB ASN E1178 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.70e-02 3.46e+03 8.23e-01 bond pdb=" N ILE F1179 " pdb=" CA ILE F1179 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.25e-02 6.40e+03 8.17e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.98e-01 ... (remaining 2416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.67: 3048 0.67 - 1.34: 169 1.34 - 2.00: 35 2.00 - 2.67: 6 2.67 - 3.34: 6 Bond angle restraints: 3264 Sorted by residual: angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 113.20 111.55 1.65 9.60e-01 1.09e+00 2.96e+00 angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 113.20 111.56 1.64 9.60e-01 1.09e+00 2.93e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 113.20 111.57 1.63 9.60e-01 1.09e+00 2.87e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 117.44 -3.34 2.00e+00 2.50e-01 2.79e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.71e+00 ... (remaining 3259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1400 16.80 - 33.60: 88 33.60 - 50.40: 15 50.40 - 67.21: 6 67.21 - 84.01: 9 Dihedral angle restraints: 1518 sinusoidal: 588 harmonic: 930 Sorted by residual: dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -180.00 -137.17 -42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.20 -42.80 2 1.50e+01 4.44e-03 9.85e+00 dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual 180.00 -137.21 -42.79 2 1.50e+01 4.44e-03 9.85e+00 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 175 0.021 - 0.043: 156 0.043 - 0.064: 66 0.064 - 0.085: 11 0.085 - 0.106: 6 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.74e-01 chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 411 not shown) Planarity restraints: 429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.100 9.50e-02 1.11e+02 4.50e-02 1.49e+00 pdb=" NE ARG B 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 983 " 0.099 9.50e-02 1.11e+02 4.47e-02 1.46e+00 pdb=" NE ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 983 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 983 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 983 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.098 9.50e-02 1.11e+02 4.43e-02 1.43e+00 pdb=" NE ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.001 2.00e-02 2.50e+03 ... (remaining 426 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 818 2.85 - 3.36: 2698 3.36 - 3.88: 4086 3.88 - 4.39: 4441 4.39 - 4.90: 7889 Nonbonded interactions: 19932 Sorted by model distance: nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.339 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.340 3.040 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.340 3.040 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.354 3.040 nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.354 3.040 ... (remaining 19927 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1166 through 1200) selection = (chain 'F' and resid 1166 through 1200) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2421 Z= 0.295 Angle : 0.396 3.339 3264 Z= 0.240 Chirality : 0.034 0.106 414 Planarity : 0.004 0.045 429 Dihedral : 14.232 84.007 904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.43), residues: 310 helix: 2.17 (0.28), residues: 246 sheet: None (None), residues: 0 loop : -1.64 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 983 PHE 0.006 0.001 PHE A 970 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 2421) covalent geometry : angle 0.39574 ( 3264) hydrogen bonds : bond 0.07266 ( 235) hydrogen bonds : angle 2.78706 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.3319 time to fit residues: 8.3832 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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: 0.1980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 949 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.140735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.122749 restraints weight = 3092.628| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.72 r_work: 0.3996 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2421 Z= 0.138 Angle : 0.315 3.056 3264 Z= 0.182 Chirality : 0.032 0.102 414 Planarity : 0.002 0.014 429 Dihedral : 2.981 9.142 322 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 3.93 % Favored : 95.71 % 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: 4.71 (0.45), residues: 310 helix: 4.05 (0.28), residues: 243 sheet: None (None), residues: 0 loop : -0.84 (0.77), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 983 PHE 0.008 0.001 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2421) covalent geometry : angle 0.31461 ( 3264) hydrogen bonds : bond 0.03303 ( 235) hydrogen bonds : angle 2.40964 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.095 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.3768 time to fit residues: 7.8837 Evaluate side-chains 19 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 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 = 0.4434 r_free = 0.4434 target = 0.148876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.132156 restraints weight = 3139.971| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.67 r_work: 0.4041 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2421 Z= 0.180 Angle : 0.326 2.687 3264 Z= 0.187 Chirality : 0.033 0.110 414 Planarity : 0.002 0.009 429 Dihedral : 3.024 9.662 322 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 3.93 % Favored : 95.36 % 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: 5.12 (0.45), residues: 310 helix: 4.27 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.41 (0.83), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 983 PHE 0.006 0.001 PHE A 970 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2421) covalent geometry : angle 0.32587 ( 3264) hydrogen bonds : bond 0.03440 ( 235) hydrogen bonds : angle 2.47949 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.098 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.2878 time to fit residues: 7.2947 Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.151289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133979 restraints weight = 3009.363| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.68 r_work: 0.4061 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2421 Z= 0.165 Angle : 0.306 2.320 3264 Z= 0.176 Chirality : 0.033 0.108 414 Planarity : 0.001 0.007 429 Dihedral : 2.938 9.697 322 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 4.29 % Favored : 94.64 % 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: 5.49 (0.44), residues: 310 helix: 4.54 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.28 (0.80), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2421) covalent geometry : angle 0.30625 ( 3264) hydrogen bonds : bond 0.03374 ( 235) hydrogen bonds : angle 2.40032 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.104 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.2683 time to fit residues: 7.1142 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 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 = 0.4460 r_free = 0.4460 target = 0.150197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.132825 restraints weight = 3004.429| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.69 r_work: 0.4063 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2421 Z= 0.152 Angle : 0.293 2.313 3264 Z= 0.169 Chirality : 0.032 0.108 414 Planarity : 0.001 0.012 429 Dihedral : 2.887 9.664 322 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 5.36 % Favored : 93.57 % 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: 5.70 (0.44), residues: 310 helix: 4.68 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.18 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2421) covalent geometry : angle 0.29250 ( 3264) hydrogen bonds : bond 0.03329 ( 235) hydrogen bonds : angle 2.35930 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.098 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.2730 time to fit residues: 7.2373 Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 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 = 0.4464 r_free = 0.4464 target = 0.150729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133518 restraints weight = 2960.725| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.67 r_work: 0.4072 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2421 Z= 0.131 Angle : 0.275 2.386 3264 Z= 0.161 Chirality : 0.032 0.107 414 Planarity : 0.001 0.015 429 Dihedral : 2.802 9.294 322 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.43 % Allowed : 5.36 % Favored : 93.21 % 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: 5.93 (0.43), residues: 310 helix: 4.83 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.08 (0.79), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 983 PHE 0.005 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 2421) covalent geometry : angle 0.27512 ( 3264) hydrogen bonds : bond 0.03248 ( 235) hydrogen bonds : angle 2.29487 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.103 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.2773 time to fit residues: 7.3515 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 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 = 0.4460 r_free = 0.4460 target = 0.150251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133015 restraints weight = 2980.494| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.67 r_work: 0.4067 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.143 Angle : 0.283 2.489 3264 Z= 0.165 Chirality : 0.032 0.109 414 Planarity : 0.001 0.007 429 Dihedral : 2.829 9.279 322 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.43 % Favored : 92.50 % 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: 5.63 (0.44), residues: 310 helix: 4.37 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.05 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.005 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2421) covalent geometry : angle 0.28254 ( 3264) hydrogen bonds : bond 0.03295 ( 235) hydrogen bonds : angle 2.31774 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.071 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2158 time to fit residues: 5.5109 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.133558 restraints weight = 3024.652| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.69 r_work: 0.4064 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2421 Z= 0.164 Angle : 0.298 2.585 3264 Z= 0.174 Chirality : 0.033 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.893 10.735 322 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.79 % Favored : 92.14 % 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: 5.47 (0.44), residues: 310 helix: 4.25 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.03 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2421) covalent geometry : angle 0.29801 ( 3264) hydrogen bonds : bond 0.03357 ( 235) hydrogen bonds : angle 2.40470 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.101 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2427 time to fit residues: 6.1798 Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 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 = 0.4421 r_free = 0.4421 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.124628 restraints weight = 3034.100| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.72 r_work: 0.4057 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.139 Angle : 0.279 2.516 3264 Z= 0.164 Chirality : 0.032 0.108 414 Planarity : 0.001 0.006 429 Dihedral : 2.819 10.307 322 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 6.79 % Favored : 92.14 % 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: 5.65 (0.43), residues: 310 helix: 4.37 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.09 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2421) covalent geometry : angle 0.27944 ( 3264) hydrogen bonds : bond 0.03281 ( 235) hydrogen bonds : angle 2.34020 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.123 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.2864 time to fit residues: 6.9814 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.143071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.124076 restraints weight = 3083.748| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.77 r_work: 0.4018 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2421 Z= 0.160 Angle : 0.294 2.476 3264 Z= 0.172 Chirality : 0.033 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.874 10.279 322 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 7.50 % Favored : 91.79 % 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: 5.55 (0.44), residues: 310 helix: 4.29 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.10 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2421) covalent geometry : angle 0.29441 ( 3264) hydrogen bonds : bond 0.03354 ( 235) hydrogen bonds : angle 2.38802 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.102 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.3020 time to fit residues: 7.0251 Evaluate side-chains 24 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1175 SER Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 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 = 0.4424 r_free = 0.4424 target = 0.143181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.124350 restraints weight = 3032.221| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.74 r_work: 0.4052 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2421 Z= 0.143 Angle : 0.281 2.455 3264 Z= 0.165 Chirality : 0.032 0.109 414 Planarity : 0.001 0.006 429 Dihedral : 2.829 10.219 322 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 7.50 % Favored : 91.43 % 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: 5.67 (0.44), residues: 310 helix: 4.37 (0.27), residues: 255 sheet: None (None), residues: 0 loop : 0.16 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.006 0.001 PHE B 927 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2421) covalent geometry : angle 0.28077 ( 3264) hydrogen bonds : bond 0.03304 ( 235) hydrogen bonds : angle 2.35157 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1298.76 seconds wall clock time: 22 minutes 48.90 seconds (1368.90 seconds total)