Starting phenix.real_space_refine on Mon Feb 10 20:55:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzv_24779/02_2025/7rzv_24779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzv_24779/02_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_24779/02_2025/7rzv_24779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzv_24779/02_2025/7rzv_24779.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzv_24779/02_2025/7rzv_24779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzv_24779/02_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-5592/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: 1.92, per 1000 atoms: 0.75 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: 0.60 Conformation dependent library (CDL) restraints added in 247.1 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: 0.20 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: 0.69 Time building geometry restraints manager: 0.68 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- 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 : 0.271 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: 0.6921 time to fit residues: 21.1641 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 : 0.290 ------------------------------------------------------------------------------- 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 = 0.132637 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: 0.3833 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.294 Fit side-chains REVERT: B 966 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8516 (mm) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5351 time to fit residues: 13.7894 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 : 0.289 ------------------------------------------------------------------------------- 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: 0.2980 chunk 8 optimal weight: 0.1980 chunk 30 optimal weight: 0.0050 chunk 14 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2212 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133156 restraints weight = 3099.660| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.65 r_work: 0.4003 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2571 Z= 0.110 Angle : 0.255 3.028 3471 Z= 0.155 Chirality : 0.030 0.104 432 Planarity : 0.001 0.015 459 Dihedral : 2.548 7.719 339 Min Nonbonded Distance : 2.510 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: 6.15 (0.42), residues: 327 helix: 5.27 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.28 (0.65), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.003 0.000 PHE E1176 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 : 0.301 Fit side-chains REVERT: B 966 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8498 (mm) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.5072 time to fit residues: 13.6945 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 : 0.278 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.148921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.129860 restraints weight = 3105.607| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.66 r_work: 0.3977 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2571 Z= 0.243 Angle : 0.306 3.139 3471 Z= 0.180 Chirality : 0.032 0.105 432 Planarity : 0.002 0.019 459 Dihedral : 2.847 9.506 339 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 6.73 % Favored : 91.25 % 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: 4.90 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.14 (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 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 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8555 (mm) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.5151 time to fit residues: 13.9208 Evaluate side-chains 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 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 Chi-restraints excluded: chain F residue 1175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.129409 restraints weight = 3100.781| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.66 r_work: 0.3976 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2571 Z= 0.249 Angle : 0.309 3.045 3471 Z= 0.180 Chirality : 0.032 0.105 432 Planarity : 0.001 0.008 459 Dihedral : 2.879 9.477 339 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.07 % Favored : 91.25 % 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: 5.65 (0.42), residues: 327 helix: 4.80 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -0.04 (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 0.001 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 28 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (mm) REVERT: B 977 LEU cc_start: 0.8669 (tp) cc_final: 0.8438 (tt) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.5000 time to fit residues: 13.5148 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 : 0.313 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.148812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.129817 restraints weight = 3109.505| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.67 r_work: 0.3976 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1802 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= 0.237 Angle : 0.318 3.789 3471 Z= 0.187 Chirality : 0.032 0.105 432 Planarity : 0.001 0.006 459 Dihedral : 2.865 9.414 339 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 7.41 % 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: 5.73 (0.42), residues: 327 helix: 4.82 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.11 (0.68), 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 0.001 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 29 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (mm) REVERT: B 977 LEU cc_start: 0.8691 (tp) cc_final: 0.8450 (tt) outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.4907 time to fit residues: 13.8004 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 : 0.269 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.148831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.129766 restraints weight = 3157.067| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.70 r_work: 0.3969 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1869 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= 0.230 Angle : 0.318 4.037 3471 Z= 0.188 Chirality : 0.032 0.105 432 Planarity : 0.001 0.006 459 Dihedral : 2.863 9.373 339 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 7.74 % 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: 5.75 (0.42), residues: 327 helix: 4.81 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.22 (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 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 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 966 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8556 (mm) REVERT: B 977 LEU cc_start: 0.8701 (tp) cc_final: 0.8447 (tt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.5059 time to fit residues: 13.6176 Evaluate side-chains 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 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 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: 2.9990 chunk 30 optimal weight: 0.0050 chunk 8 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.0670 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 949 GLN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.150382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.131345 restraints weight = 3115.117| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.68 r_work: 0.3998 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2571 Z= 0.123 Angle : 0.287 4.474 3471 Z= 0.173 Chirality : 0.030 0.106 432 Planarity : 0.001 0.005 459 Dihedral : 2.599 7.978 339 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.72 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: 5.82 (0.43), residues: 327 helix: 4.55 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.24 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.004 0.001 PHE E1176 ARG 0.000 0.000 ARG F1185 *********************** 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 27 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.306 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.4944 time to fit residues: 13.3773 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 : 0.304 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 949 GLN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.129924 restraints weight = 3128.397| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.66 r_work: 0.3982 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2571 Z= 0.251 Angle : 0.351 5.541 3471 Z= 0.198 Chirality : 0.033 0.106 432 Planarity : 0.001 0.006 459 Dihedral : 2.871 9.949 339 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.42 % 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: 5.89 (0.42), residues: 327 helix: 4.89 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.34 (0.70), 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 0.001 0.000 ARG D1185 *********************** 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 26 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8650 (tp) cc_final: 0.8432 (tt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.5095 time to fit residues: 13.7293 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 : 0.286 ------------------------------------------------------------------------------- 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: 0.6980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.149471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.130370 restraints weight = 3069.145| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.65 r_work: 0.3989 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1958 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= 0.199 Angle : 0.331 5.278 3471 Z= 0.189 Chirality : 0.032 0.106 432 Planarity : 0.001 0.006 459 Dihedral : 2.805 9.284 339 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.69 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: 5.53 (0.42), residues: 327 helix: 4.30 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.41 (0.68), residues: 63 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 : 0.269 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.5114 time to fit residues: 13.7820 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 : 0.258 ------------------------------------------------------------------------------- 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: 0.3980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 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 = 0.4402 r_free = 0.4402 target = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.130076 restraints weight = 3101.188| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.67 r_work: 0.3981 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2571 Z= 0.224 Angle : 0.338 5.133 3471 Z= 0.193 Chirality : 0.032 0.106 432 Planarity : 0.001 0.006 459 Dihedral : 2.863 9.718 339 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.69 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: 5.91 (0.42), residues: 327 helix: 4.88 (0.25), residues: 246 sheet: None (None), residues: 0 loop : 0.46 (0.70), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.52 seconds wall clock time: 41 minutes 19.17 seconds (2479.17 seconds total)