Starting phenix.real_space_refine on Wed Mar 5 15:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzs_24776/03_2025/7rzs_24776.cif" } resolution = 2.52 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 1509 2.51 5 N 426 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2445 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 534 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Restraints were copied for chains: D, F, C, B Time building chain proxies: 1.66, per 1000 atoms: 0.68 Number of scatterers: 2445 At special positions: 0 Unit cell: (50.6075, 42.445, 115.908, 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 510 8.00 N 426 7.00 C 1509 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: 0.65 Conformation dependent library (CDL) restraints added in 308.9 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 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: 3.569A 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: 3.569A 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: 3.570A 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: 0.63 Time building geometry restraints manager: 0.78 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: 465 1.29 - 1.35: 399 1.35 - 1.41: 63 1.41 - 1.48: 366 1.48 - 1.54: 1155 Bond restraints: 2448 Sorted by residual: bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.83e-01 bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.37e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.34e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.87e-01 bond pdb=" N ILE E1179 " pdb=" CA ILE E1179 " ideal model delta sigma weight residual 1.459 1.450 0.009 1.25e-02 6.40e+03 5.42e-01 ... (remaining 2443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 3173 0.93 - 1.87: 100 1.87 - 2.80: 15 2.80 - 3.74: 6 3.74 - 4.67: 6 Bond angle restraints: 3300 Sorted by residual: angle pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " pdb=" CG ARG B 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.44e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.34e+00 angle pdb=" C ARG C 983 " pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " ideal model delta sigma weight residual 110.31 113.88 -3.57 2.09e+00 2.29e-01 2.92e+00 angle pdb=" C ARG B 983 " pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " ideal model delta sigma weight residual 110.31 113.86 -3.55 2.09e+00 2.29e-01 2.89e+00 ... (remaining 3295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1389 17.76 - 35.52: 111 35.52 - 53.28: 12 53.28 - 71.05: 9 71.05 - 88.81: 6 Dihedral angle restraints: 1527 sinusoidal: 591 harmonic: 936 Sorted by residual: dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.02 40.02 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 212 0.023 - 0.046: 134 0.046 - 0.068: 53 0.068 - 0.091: 7 0.091 - 0.114: 8 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA PHE C 970 " pdb=" N PHE C 970 " pdb=" C PHE C 970 " pdb=" CB PHE C 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.24e-01 chirality pdb=" CA PHE A 970 " pdb=" N PHE A 970 " pdb=" C PHE A 970 " pdb=" CB PHE A 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA PHE B 970 " pdb=" N PHE B 970 " pdb=" C PHE B 970 " pdb=" CB PHE B 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 411 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 983 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 983 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 984 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 983 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG C 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 984 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 983 " -0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ARG B 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 984 " -0.008 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 600 2.80 - 3.32: 2636 3.32 - 3.85: 4135 3.85 - 4.37: 4614 4.37 - 4.90: 8090 Nonbonded interactions: 20075 Sorted by model distance: nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.273 3.040 nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.273 3.040 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.273 3.040 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.506 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.507 3.120 ... (remaining 20070 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.050 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.022 2448 Z= 0.315 Angle : 0.461 4.674 3300 Z= 0.271 Chirality : 0.034 0.114 414 Planarity : 0.004 0.041 435 Dihedral : 14.727 88.807 909 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 1.98 (0.43), residues: 312 helix: 2.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.53 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE B 970 ARG 0.011 0.003 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 980 ILE cc_start: 0.8695 (mt) cc_final: 0.8461 (mt) REVERT: C 965 GLN cc_start: 0.8146 (mm110) cc_final: 0.7903 (mm110) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.5924 time to fit residues: 20.0498 Evaluate side-chains 32 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 965 GLN B 935 GLN B 978 ASN C 978 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.142628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.128196 restraints weight = 3112.182| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.11 r_work: 0.3934 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2448 Z= 0.205 Angle : 0.364 4.167 3300 Z= 0.203 Chirality : 0.034 0.096 414 Planarity : 0.002 0.024 435 Dihedral : 3.284 11.313 324 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 7.45 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.17 (0.44), residues: 312 helix: 3.62 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.95 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 970 ARG 0.007 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.5600 time to fit residues: 17.9562 Evaluate side-chains 30 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 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 = 0.4287 r_free = 0.4287 target = 0.142990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.128529 restraints weight = 3138.673| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.12 r_work: 0.3929 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2448 Z= 0.233 Angle : 0.360 6.222 3300 Z= 0.200 Chirality : 0.034 0.099 414 Planarity : 0.002 0.036 435 Dihedral : 3.169 10.193 324 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 10.28 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.98 (0.44), residues: 312 helix: 4.18 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.58 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 938 ARG 0.005 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.279 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.5576 time to fit residues: 16.5878 Evaluate side-chains 28 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.142056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127492 restraints weight = 3109.294| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.16 r_work: 0.3906 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2448 Z= 0.187 Angle : 0.329 6.120 3300 Z= 0.185 Chirality : 0.033 0.099 414 Planarity : 0.003 0.041 435 Dihedral : 3.027 9.756 324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 10.28 % Favored : 88.65 % 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: 5.37 (0.43), residues: 312 helix: 4.44 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.41 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 970 ARG 0.006 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.5540 time to fit residues: 17.0660 Evaluate side-chains 29 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.141032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.126307 restraints weight = 3197.483| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.20 r_work: 0.3885 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2448 Z= 0.245 Angle : 0.372 6.459 3300 Z= 0.202 Chirality : 0.035 0.136 414 Planarity : 0.002 0.015 435 Dihedral : 3.083 10.087 324 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 10.99 % Favored : 87.94 % 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: 5.25 (0.43), residues: 312 helix: 4.35 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.41 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 938 ARG 0.003 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.296 Fit side-chains REVERT: C 970 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8279 (m-10) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.7412 time to fit residues: 22.6097 Evaluate side-chains 29 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.140773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.126210 restraints weight = 3184.251| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.20 r_work: 0.3884 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2448 Z= 0.216 Angle : 0.364 6.748 3300 Z= 0.192 Chirality : 0.034 0.148 414 Planarity : 0.002 0.010 435 Dihedral : 2.981 9.783 324 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 10.28 % Favored : 87.94 % 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: 5.33 (0.43), residues: 312 helix: 4.48 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.48 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE B 970 ARG 0.004 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 970 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8284 (m-10) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 0.5337 time to fit residues: 16.9882 Evaluate side-chains 30 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.139968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.125288 restraints weight = 3241.589| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.25 r_work: 0.3875 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2448 Z= 0.271 Angle : 0.389 7.107 3300 Z= 0.204 Chirality : 0.036 0.207 414 Planarity : 0.002 0.011 435 Dihedral : 3.093 10.316 324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 10.99 % Favored : 87.23 % 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: 312 helix: 4.30 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.38 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE B 938 ARG 0.002 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: C 970 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8326 (m-10) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.6474 time to fit residues: 21.8364 Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.125991 restraints weight = 3240.068| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.24 r_work: 0.3876 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2448 Z= 0.249 Angle : 0.404 7.325 3300 Z= 0.210 Chirality : 0.036 0.203 414 Planarity : 0.002 0.008 435 Dihedral : 3.075 10.617 324 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 10.99 % Favored : 87.59 % 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: 5.08 (0.44), residues: 312 helix: 4.27 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 938 ARG 0.006 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: C 970 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (m-10) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.6275 time to fit residues: 21.2013 Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.140300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.125688 restraints weight = 3221.736| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.23 r_work: 0.3878 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2448 Z= 0.257 Angle : 0.413 7.064 3300 Z= 0.214 Chirality : 0.036 0.195 414 Planarity : 0.002 0.019 435 Dihedral : 3.114 10.996 324 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.77 % Allowed : 10.99 % Favored : 87.23 % 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: 5.05 (0.44), residues: 312 helix: 4.24 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.37 (0.77), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 938 ARG 0.006 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: C 970 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (m-10) outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.6413 time to fit residues: 21.6527 Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126134 restraints weight = 3188.410| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.19 r_work: 0.3890 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2448 Z= 0.211 Angle : 0.400 7.571 3300 Z= 0.206 Chirality : 0.035 0.198 414 Planarity : 0.002 0.029 435 Dihedral : 3.056 11.889 324 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 12.06 % Favored : 86.52 % 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: 5.21 (0.44), residues: 312 helix: 4.34 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.28 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 938 ARG 0.005 0.001 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: C 970 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8301 (m-10) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.6396 time to fit residues: 21.5715 Evaluate side-chains 33 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 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 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.140594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126100 restraints weight = 3241.022| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.23 r_work: 0.3881 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2448 Z= 0.244 Angle : 0.406 7.576 3300 Z= 0.210 Chirality : 0.036 0.194 414 Planarity : 0.002 0.016 435 Dihedral : 3.101 12.491 324 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % Favored : 86.88 % 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: 5.10 (0.44), residues: 312 helix: 4.26 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.31 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 938 ARG 0.005 0.001 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.57 seconds wall clock time: 34 minutes 2.96 seconds (2042.96 seconds total)