Starting phenix.real_space_refine on Wed Mar 5 15:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzv_24779/03_2025/7rzv_24779.cif" } resolution = 2.11 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= 0.019 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 1578 2.51 5 N 447 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2562 Number of models: 1 Model: "" Number of chains: 2 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: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: D, F, C, B Time building chain proxies: 1.86, per 1000 atoms: 0.73 Number of scatterers: 2562 At special positions: 0 Unit cell: (53.8725, 42.445, 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 537 8.00 N 447 7.00 C 1578 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: 0.62 Conformation dependent library (CDL) restraints added in 297.4 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 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 removed outlier: 3.649A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.649A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.649A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 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: 0.73 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: 1.23 - 1.29: 486 1.29 - 1.35: 420 1.35 - 1.42: 82 1.42 - 1.48: 380 1.48 - 1.54: 1203 Bond restraints: 2571 Sorted by residual: bond pdb=" CG LEU B 977 " pdb=" CD1 LEU B 977 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.14e-01 bond pdb=" CG LEU C 977 " pdb=" CD1 LEU C 977 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CG LEU A 977 " pdb=" CD1 LEU A 977 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.79e-01 bond pdb=" CG LEU B 966 " pdb=" CD2 LEU B 966 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.26e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.16e-01 ... (remaining 2566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 3340 0.73 - 1.45: 112 1.45 - 2.18: 7 2.18 - 2.90: 6 2.90 - 3.63: 6 Bond angle restraints: 3471 Sorted by residual: angle pdb=" CB LEU B 977 " pdb=" CG LEU B 977 " pdb=" CD1 LEU B 977 " ideal model delta sigma weight residual 110.70 114.33 -3.63 3.00e+00 1.11e-01 1.46e+00 angle pdb=" CB LEU A 977 " pdb=" CG LEU A 977 " pdb=" CD1 LEU A 977 " ideal model delta sigma weight residual 110.70 114.29 -3.59 3.00e+00 1.11e-01 1.43e+00 angle pdb=" CB LEU C 977 " pdb=" CG LEU C 977 " pdb=" CD1 LEU C 977 " ideal model delta sigma weight residual 110.70 114.26 -3.56 3.00e+00 1.11e-01 1.41e+00 angle pdb=" C LEU A 977 " pdb=" N ASN A 978 " pdb=" CA ASN A 978 " ideal model delta sigma weight residual 120.29 118.73 1.56 1.42e+00 4.96e-01 1.21e+00 angle pdb=" C LEU B 977 " pdb=" N ASN B 978 " pdb=" CA ASN B 978 " ideal model delta sigma weight residual 120.29 118.73 1.56 1.42e+00 4.96e-01 1.20e+00 ... (remaining 3466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1461 17.81 - 35.63: 114 35.63 - 53.44: 9 53.44 - 71.25: 12 71.25 - 89.07: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ARG D1185 " pdb=" CB ARG D1185 " pdb=" CG ARG D1185 " pdb=" CD ARG D1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.79 -39.79 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA ARG E1185 " pdb=" CB ARG E1185 " pdb=" CG ARG E1185 " pdb=" CD ARG E1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.77 -39.77 3 1.50e+01 4.44e-03 7.06e+00 dihedral pdb=" CA ARG F1185 " pdb=" CB ARG F1185 " pdb=" CG ARG F1185 " pdb=" CD ARG F1185 " ideal model delta sinusoidal sigma weight residual 60.00 99.76 -39.76 3 1.50e+01 4.44e-03 7.06e+00 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 208 0.022 - 0.043: 159 0.043 - 0.065: 41 0.065 - 0.086: 7 0.086 - 0.108: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA LEU A 977 " pdb=" N LEU A 977 " pdb=" C LEU A 977 " pdb=" CB LEU A 977 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA LEU B 977 " pdb=" N LEU B 977 " pdb=" C LEU B 977 " pdb=" CB LEU B 977 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CA LEU C 977 " pdb=" N LEU C 977 " pdb=" C LEU C 977 " pdb=" CB LEU C 977 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 429 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F1177 " -0.002 2.00e-02 2.50e+03 5.03e-03 2.53e-01 pdb=" C VAL F1177 " 0.009 2.00e-02 2.50e+03 pdb=" O VAL F1177 " -0.003 2.00e-02 2.50e+03 pdb=" N ASN F1178 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1177 " 0.002 2.00e-02 2.50e+03 4.94e-03 2.45e-01 pdb=" C VAL E1177 " -0.009 2.00e-02 2.50e+03 pdb=" O VAL E1177 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN E1178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.002 2.00e-02 2.50e+03 4.90e-03 2.40e-01 pdb=" C VAL C 952 " -0.008 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.003 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 873 2.86 - 3.37: 2778 3.37 - 3.88: 4432 3.88 - 4.39: 4741 4.39 - 4.90: 8106 Nonbonded interactions: 20930 Sorted by model distance: nonbonded pdb=" OG SER C 943 " pdb=" OE2 GLU E1182 " model vdw 2.348 3.040 nonbonded pdb=" OG SER B 943 " pdb=" OE2 GLU D1182 " model vdw 2.348 3.040 nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.372 3.040 nonbonded pdb=" OD1 ASP F1163 " pdb=" N VAL F1164 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP E1163 " pdb=" N VAL E1164 " model vdw 2.395 3.120 ... (remaining 20925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.250 Find NCS groups from input model: 0.040 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.005 0.026 2571 Z= 0.319 Angle : 0.354 3.628 3471 Z= 0.203 Chirality : 0.034 0.108 432 Planarity : 0.002 0.012 459 Dihedral : 14.679 89.066 954 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.06 (0.43), residues: 327 helix: 3.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.36 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.002 0.001 PHE E1176 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 978 ASN cc_start: 0.7770 (m-40) cc_final: 0.7421 (m-40) REVERT: B 969 ASN cc_start: 0.7937 (m-40) cc_final: 0.7733 (m-40) REVERT: D 1187 ASN cc_start: 0.8454 (m-40) cc_final: 0.8228 (m-40) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.6625 time to fit residues: 20.3183 Evaluate side-chains 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 935 GLN B 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.151779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.132639 restraints weight = 3080.732| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.66 r_work: 0.3990 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2571 Z= 0.166 Angle : 0.277 2.703 3471 Z= 0.159 Chirality : 0.031 0.106 432 Planarity : 0.001 0.011 459 Dihedral : 2.806 9.297 339 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 5.72 % Favored : 93.60 % 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: 5.20 (0.43), residues: 327 helix: 4.61 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.72 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E1159 PHE 0.005 0.001 PHE A 970 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.276 Fit side-chains REVERT: B 966 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8521 (mm) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5119 time to fit residues: 13.3117 Evaluate side-chains 24 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 30 optimal weight: 0.0870 chunk 14 optimal weight: 0.0070 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.151977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.133003 restraints weight = 3098.764| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.65 r_work: 0.4003 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2571 Z= 0.118 Angle : 0.258 3.039 3471 Z= 0.156 Chirality : 0.030 0.104 432 Planarity : 0.001 0.015 459 Dihedral : 2.574 7.780 339 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 6.73 % Favored : 91.92 % 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: 6.08 (0.42), residues: 327 helix: 5.22 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.29 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.003 0.001 PHE A 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.275 Fit side-chains REVERT: B 966 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8522 (mm) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.4845 time to fit residues: 13.0901 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.150155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.131103 restraints weight = 3103.048| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.65 r_work: 0.3995 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2571 Z= 0.147 Angle : 0.266 3.090 3471 Z= 0.161 Chirality : 0.031 0.105 432 Planarity : 0.001 0.011 459 Dihedral : 2.601 8.014 339 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 7.41 % Favored : 91.58 % 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: 6.17 (0.42), residues: 327 helix: 5.22 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.03 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8548 (mm) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5182 time to fit residues: 13.9151 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.148867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.129659 restraints weight = 3102.741| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.68 r_work: 0.3977 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2571 Z= 0.250 Angle : 0.308 3.055 3471 Z= 0.179 Chirality : 0.032 0.106 432 Planarity : 0.002 0.016 459 Dihedral : 2.836 9.432 339 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.58 % 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: 5.79 (0.42), residues: 327 helix: 4.89 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.03 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.008 0.001 PHE E1176 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8559 (mm) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.5246 time to fit residues: 14.7093 Evaluate side-chains 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 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 = 0.4400 r_free = 0.4400 target = 0.148844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.129894 restraints weight = 3113.005| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.65 r_work: 0.3982 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2571 Z= 0.223 Angle : 0.309 3.749 3471 Z= 0.182 Chirality : 0.032 0.104 432 Planarity : 0.001 0.006 459 Dihedral : 2.788 9.158 339 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.41 % Favored : 90.91 % 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: 5.87 (0.42), residues: 327 helix: 4.92 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.17 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.007 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 977 LEU cc_start: 0.8679 (tp) cc_final: 0.8445 (tt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.5428 time to fit residues: 14.6142 Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain F residue 1175 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 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 = 0.4394 r_free = 0.4394 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.129306 restraints weight = 3156.944| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.71 r_work: 0.3969 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2571 Z= 0.265 Angle : 0.334 4.097 3471 Z= 0.194 Chirality : 0.033 0.104 432 Planarity : 0.001 0.007 459 Dihedral : 2.915 9.899 339 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.41 % Favored : 90.91 % 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: 5.71 (0.42), residues: 327 helix: 4.77 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.23 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.009 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8584 (mm) REVERT: B 977 LEU cc_start: 0.8705 (tp) cc_final: 0.8472 (tt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.5036 time to fit residues: 13.6354 Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain F residue 1175 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 8 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.150091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.131084 restraints weight = 3111.015| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.66 r_work: 0.3997 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2571 Z= 0.142 Angle : 0.292 4.467 3471 Z= 0.175 Chirality : 0.031 0.105 432 Planarity : 0.001 0.005 459 Dihedral : 2.636 8.185 339 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.08 % Favored : 90.91 % 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: 5.74 (0.42), residues: 327 helix: 4.50 (0.27), residues: 264 sheet: None (None), residues: 0 loop : 0.23 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE E1176 ARG 0.000 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8633 (tp) cc_final: 0.8404 (tt) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.5207 time to fit residues: 14.0258 Evaluate side-chains 25 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.148475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.129332 restraints weight = 3130.144| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.67 r_work: 0.3973 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2571 Z= 0.305 Angle : 0.376 5.664 3471 Z= 0.210 Chirality : 0.034 0.105 432 Planarity : 0.002 0.007 459 Dihedral : 2.992 10.718 339 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 8.08 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.68 (0.42), residues: 327 helix: 4.72 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.34 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.010 0.002 PHE E1176 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8676 (tp) cc_final: 0.8458 (tt) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.5014 time to fit residues: 13.5472 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain F residue 1175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 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 = 0.4406 r_free = 0.4406 target = 0.149346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.130355 restraints weight = 3076.864| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.64 r_work: 0.3990 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2571 Z= 0.193 Angle : 0.331 5.243 3471 Z= 0.190 Chirality : 0.032 0.106 432 Planarity : 0.001 0.006 459 Dihedral : 2.806 9.268 339 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 9.09 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.00 (0.42), residues: 327 helix: 4.95 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.45 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8641 (tp) cc_final: 0.8420 (tt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.5159 time to fit residues: 13.9135 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain F residue 1175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.130695 restraints weight = 3104.846| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.66 r_work: 0.3992 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2571 Z= 0.163 Angle : 0.315 4.775 3471 Z= 0.183 Chirality : 0.031 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.699 8.572 339 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.75 % Favored : 90.24 % 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: 5.73 (0.42), residues: 327 helix: 4.44 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.45 (0.69), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE E1176 ARG 0.001 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.23 seconds wall clock time: 42 minutes 39.57 seconds (2559.57 seconds total)