Starting phenix.real_space_refine on Fri Aug 22 12:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fa1_28947/08_2025/8fa1_28947.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 1572 2.51 5 N 447 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: B, C, E, F Time building chain proxies: 0.48, per 1000 atoms: 0.19 Number of scatterers: 2553 At special positions: 0 Unit cell: (47.436, 55.476, 118.992, 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 534 8.00 N 447 7.00 C 1572 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: 0.13 Conformation dependent library (CDL) restraints added in 59.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.04 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: 3.776A 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: 3.776A 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: 3.776A 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: 0.23 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 483 1.29 - 1.35: 417 1.35 - 1.42: 66 1.42 - 1.48: 378 1.48 - 1.54: 1215 Bond restraints: 2559 Sorted by residual: bond pdb=" CA ASN D1178 " pdb=" CB ASN D1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.58e-01 bond pdb=" CA ASN F1178 " pdb=" CB ASN F1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.49e-01 bond pdb=" CB VAL E1177 " pdb=" CG2 VAL E1177 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.48e-01 bond pdb=" CB VAL F1177 " pdb=" CG2 VAL F1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.42e-01 bond pdb=" CB VAL D1177 " pdb=" CG2 VAL D1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.30e-01 ... (remaining 2554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 3351 1.35 - 2.70: 79 2.70 - 4.04: 14 4.04 - 5.39: 3 5.39 - 6.74: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" N ASN A 978 " pdb=" CA ASN A 978 " pdb=" CB ASN A 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.19e+00 angle pdb=" N ASN B 978 " pdb=" CA ASN B 978 " pdb=" CB ASN B 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.18e+00 angle pdb=" N ASN C 978 " pdb=" CA ASN C 978 " pdb=" CB ASN C 978 " ideal model delta sigma weight residual 110.16 113.83 -3.67 1.48e+00 4.57e-01 6.14e+00 angle pdb=" CA LEU B 962 " pdb=" CB LEU B 962 " pdb=" CG LEU B 962 " ideal model delta sigma weight residual 116.30 123.04 -6.74 3.50e+00 8.16e-02 3.71e+00 angle pdb=" CA LEU A 962 " pdb=" CB LEU A 962 " pdb=" CG LEU A 962 " ideal model delta sigma weight residual 116.30 122.99 -6.69 3.50e+00 8.16e-02 3.65e+00 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1368 14.97 - 29.94: 189 29.94 - 44.91: 21 44.91 - 59.88: 18 59.88 - 74.85: 9 Dihedral angle restraints: 1605 sinusoidal: 624 harmonic: 981 Sorted by residual: dihedral pdb=" N GLN C 957 " pdb=" CA GLN C 957 " pdb=" CB GLN C 957 " pdb=" CG GLN C 957 " ideal model delta sinusoidal sigma weight residual 180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" CB GLN B 957 " pdb=" CG GLN B 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 957 " pdb=" CA GLN A 957 " pdb=" CB GLN A 957 " pdb=" CG GLN A 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.33 -59.67 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 255 0.027 - 0.053: 119 0.053 - 0.080: 36 0.080 - 0.106: 19 0.106 - 0.133: 6 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA GLN A 920 " pdb=" N GLN A 920 " pdb=" C GLN A 920 " pdb=" CB GLN A 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA GLN B 920 " pdb=" N GLN B 920 " pdb=" C GLN B 920 " pdb=" CB GLN B 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA GLN C 920 " pdb=" N GLN C 920 " pdb=" C GLN C 920 " pdb=" CB GLN C 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 432 not shown) Planarity restraints: 453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 919 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ASN A 919 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 920 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 919 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ASN B 919 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN B 919 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 920 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 919 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C ASN C 919 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN C 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN C 920 " -0.013 2.00e-02 2.50e+03 ... (remaining 450 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 2762 3.33 - 3.85: 4259 3.85 - 4.38: 4728 4.38 - 4.90: 8073 Nonbonded interactions: 20525 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.333 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.418 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.429 3.120 ... (remaining 20520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2559 Z= 0.259 Angle : 0.572 6.742 3453 Z= 0.296 Chirality : 0.039 0.133 435 Planarity : 0.004 0.034 453 Dihedral : 15.924 74.850 957 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.42), residues: 327 helix: 1.08 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -1.33 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 983 PHE 0.003 0.001 PHE A 927 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 2559) covalent geometry : angle 0.57250 ( 3453) hydrogen bonds : bond 0.04370 ( 232) hydrogen bonds : angle 3.83599 ( 696) *********************** 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 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.058 Fit side-chains REVERT: B 980 ILE cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: C 973 ILE cc_start: 0.9020 (mt) cc_final: 0.8778 (mt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1412 time to fit residues: 5.7027 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN E1159 HIS F1159 HIS F1173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.123765 restraints weight = 3544.920| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.21 r_work: 0.3921 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2559 Z= 0.130 Angle : 0.450 7.364 3453 Z= 0.235 Chirality : 0.036 0.121 435 Planarity : 0.002 0.012 453 Dihedral : 3.271 11.314 339 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.37 % Allowed : 14.81 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.45), residues: 327 helix: 3.10 (0.29), residues: 249 sheet: None (None), residues: 0 loop : -0.41 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 983 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2559) covalent geometry : angle 0.45015 ( 3453) hydrogen bonds : bond 0.03275 ( 232) hydrogen bonds : angle 3.09291 ( 696) *********************** 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 49 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.057 Fit side-chains REVERT: C 973 ILE cc_start: 0.9064 (mt) cc_final: 0.8816 (mt) outliers start: 10 outliers final: 1 residues processed: 48 average time/residue: 0.1488 time to fit residues: 7.5348 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 32 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.142580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.124076 restraints weight = 3588.362| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.24 r_work: 0.3940 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2559 Z= 0.117 Angle : 0.434 7.688 3453 Z= 0.224 Chirality : 0.036 0.127 435 Planarity : 0.002 0.011 453 Dihedral : 3.111 9.457 339 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.68 (0.46), residues: 327 helix: 3.92 (0.29), residues: 252 sheet: None (None), residues: 0 loop : -0.09 (0.84), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 983 PHE 0.004 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2559) covalent geometry : angle 0.43415 ( 3453) hydrogen bonds : bond 0.03146 ( 232) hydrogen bonds : angle 2.85587 ( 696) *********************** 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 45 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.077 Fit side-chains REVERT: C 973 ILE cc_start: 0.9082 (mt) cc_final: 0.8836 (mt) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.2458 time to fit residues: 11.1007 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1177 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 25 optimal weight: 0.0040 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.142268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.124105 restraints weight = 3588.488| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.21 r_work: 0.3926 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2559 Z= 0.136 Angle : 0.428 7.349 3453 Z= 0.226 Chirality : 0.036 0.132 435 Planarity : 0.002 0.016 453 Dihedral : 3.067 9.577 339 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.36 % Allowed : 16.16 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.80 (0.46), residues: 327 helix: 4.05 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.06 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.005 0.001 PHE C 970 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2559) covalent geometry : angle 0.42779 ( 3453) hydrogen bonds : bond 0.03196 ( 232) hydrogen bonds : angle 2.82899 ( 696) *********************** 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 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.094 Fit side-chains REVERT: C 973 ILE cc_start: 0.9077 (mt) cc_final: 0.8826 (mt) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.2246 time to fit residues: 10.8765 Evaluate side-chains 45 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain D residue 1177 VAL Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.143502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.125333 restraints weight = 3488.002| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.21 r_work: 0.3939 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2559 Z= 0.118 Angle : 0.425 7.053 3453 Z= 0.223 Chirality : 0.036 0.133 435 Planarity : 0.002 0.013 453 Dihedral : 2.982 8.985 339 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.36 % Allowed : 15.15 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.02 (0.45), residues: 327 helix: 4.21 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.03 (0.83), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.004 0.001 PHE C 970 HIS 0.001 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2559) covalent geometry : angle 0.42458 ( 3453) hydrogen bonds : bond 0.03161 ( 232) hydrogen bonds : angle 2.77521 ( 696) *********************** 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 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.101 Fit side-chains REVERT: C 973 ILE cc_start: 0.9078 (mt) cc_final: 0.8823 (mt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.2811 time to fit residues: 13.2258 Evaluate side-chains 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 5 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 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.141475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.123286 restraints weight = 3565.988| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.19 r_work: 0.3914 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2559 Z= 0.175 Angle : 0.457 6.964 3453 Z= 0.244 Chirality : 0.038 0.133 435 Planarity : 0.002 0.012 453 Dihedral : 3.143 9.825 339 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.36 % Allowed : 16.50 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.63 (0.45), residues: 327 helix: 3.92 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.07 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 983 PHE 0.004 0.001 PHE A 927 HIS 0.000 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2559) covalent geometry : angle 0.45728 ( 3453) hydrogen bonds : bond 0.03266 ( 232) hydrogen bonds : angle 2.91747 ( 696) *********************** 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 47 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.100 Fit side-chains REVERT: C 973 ILE cc_start: 0.9057 (mt) cc_final: 0.8794 (mt) outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 0.2999 time to fit residues: 13.7916 Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.148055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.130152 restraints weight = 3449.877| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.10 r_work: 0.3948 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2559 Z= 0.135 Angle : 0.436 7.468 3453 Z= 0.234 Chirality : 0.037 0.145 435 Planarity : 0.002 0.013 453 Dihedral : 3.045 9.314 339 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.68 % Allowed : 17.17 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.81 (0.45), residues: 327 helix: 4.05 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.01 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.004 0.001 PHE A 927 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2559) covalent geometry : angle 0.43636 ( 3453) hydrogen bonds : bond 0.03201 ( 232) hydrogen bonds : angle 2.83066 ( 696) *********************** 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 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.100 Fit side-chains REVERT: C 973 ILE cc_start: 0.9108 (mt) cc_final: 0.8869 (mt) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.2749 time to fit residues: 12.1044 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.124669 restraints weight = 3565.027| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.21 r_work: 0.3924 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2559 Z= 0.147 Angle : 0.452 7.415 3453 Z= 0.245 Chirality : 0.038 0.157 435 Planarity : 0.002 0.014 453 Dihedral : 3.113 10.248 339 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.68 % Allowed : 16.50 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.74 (0.45), residues: 327 helix: 4.00 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.03 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.004 0.001 PHE A 927 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2559) covalent geometry : angle 0.45207 ( 3453) hydrogen bonds : bond 0.03251 ( 232) hydrogen bonds : angle 2.93359 ( 696) *********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.106 Fit side-chains REVERT: C 973 ILE cc_start: 0.9052 (mt) cc_final: 0.8788 (mt) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.2882 time to fit residues: 12.6987 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 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 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.142444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.124210 restraints weight = 3614.257| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.22 r_work: 0.3914 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2559 Z= 0.175 Angle : 0.476 7.478 3453 Z= 0.255 Chirality : 0.039 0.147 435 Planarity : 0.002 0.015 453 Dihedral : 3.178 10.890 339 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.02 % Allowed : 17.51 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.62 (0.45), residues: 327 helix: 3.91 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.08 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.005 0.001 PHE B 970 HIS 0.000 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2559) covalent geometry : angle 0.47591 ( 3453) hydrogen bonds : bond 0.03275 ( 232) hydrogen bonds : angle 2.97545 ( 696) *********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.100 Fit side-chains REVERT: C 973 ILE cc_start: 0.9042 (mt) cc_final: 0.8778 (mt) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.2907 time to fit residues: 12.5032 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.142973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.125321 restraints weight = 3573.462| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.14 r_work: 0.3963 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2559 Z= 0.118 Angle : 0.454 7.910 3453 Z= 0.243 Chirality : 0.038 0.176 435 Planarity : 0.002 0.019 453 Dihedral : 3.086 11.793 339 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.68 % Allowed : 17.51 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.45), residues: 327 helix: 4.19 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.04 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.006 0.001 PHE B 970 HIS 0.001 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2559) covalent geometry : angle 0.45409 ( 3453) hydrogen bonds : bond 0.03207 ( 232) hydrogen bonds : angle 2.89721 ( 696) ********************** 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 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.103 Fit side-chains REVERT: C 973 ILE cc_start: 0.9122 (mt) cc_final: 0.8887 (mt) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.2828 time to fit residues: 12.4344 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.125368 restraints weight = 3544.201| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.17 r_work: 0.3937 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2559 Z= 0.172 Angle : 1.323 56.417 3453 Z= 0.790 Chirality : 0.040 0.175 435 Planarity : 0.002 0.019 453 Dihedral : 3.062 10.718 339 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.68 % Allowed : 18.18 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.89 (0.45), residues: 327 helix: 4.11 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.00 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 PHE 0.005 0.001 PHE A 927 HIS 0.001 0.000 HIS E1159 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 2559) covalent geometry : angle 1.32304 ( 3453) hydrogen bonds : bond 0.03230 ( 232) hydrogen bonds : angle 2.94053 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 931.94 seconds wall clock time: 16 minutes 50.64 seconds (1010.64 seconds total)