Starting phenix.real_space_refine on Wed Sep 17 03:01:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzt_24777/09_2025/7rzt_24777.map" } resolution = 2.35 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= 0.018 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 1518 2.51 5 N 426 2.21 5 O 507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" 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: B, C, E, F Time building chain proxies: 0.63, per 1000 atoms: 0.26 Number of scatterers: 2451 At special positions: 0 Unit cell: (48.975, 42.445, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 507 8.00 N 426 7.00 C 1518 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: 0.21 Conformation dependent library (CDL) restraints added in 97.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.27 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 - 1.42: 61 1.42 - 1.48: 365 1.48 - 1.54: 1164 Bond restraints: 2454 Sorted by residual: bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.50e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.99e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.98e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.008 1.15e-02 7.56e+03 5.44e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.228 0.009 1.19e-02 7.06e+03 5.18e-01 ... (remaining 2449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.46: 2912 0.46 - 0.91: 344 0.91 - 1.37: 39 1.37 - 1.82: 11 1.82 - 2.28: 3 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE E1169 " pdb=" CA ILE E1169 " pdb=" C ILE E1169 " ideal model delta sigma weight residual 109.34 111.62 -2.28 2.08e+00 2.31e-01 1.20e+00 angle pdb=" N ILE F1169 " pdb=" CA ILE F1169 " pdb=" C ILE F1169 " ideal model delta sigma weight residual 109.34 111.61 -2.27 2.08e+00 2.31e-01 1.19e+00 angle pdb=" CA ILE F1169 " pdb=" C ILE F1169 " pdb=" N SER F1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.69e-01 angle pdb=" CA ILE E1169 " pdb=" C ILE E1169 " pdb=" N SER E1170 " ideal model delta sigma weight residual 116.60 117.95 -1.35 1.45e+00 4.76e-01 8.61e-01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 1386 17.87 - 35.74: 120 35.74 - 53.60: 9 53.60 - 71.47: 9 71.47 - 89.34: 6 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.67 34.67 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU C 984 " pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sinusoidal sigma weight residual -60.00 -94.64 34.64 3 1.50e+01 4.44e-03 5.88e+00 dihedral pdb=" CB GLU A 918 " pdb=" CG GLU A 918 " pdb=" CD GLU A 918 " pdb=" OE1 GLU A 918 " ideal model delta sinusoidal sigma weight residual 0.00 63.30 -63.30 1 3.00e+01 1.11e-03 5.87e+00 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 179 0.020 - 0.040: 165 0.040 - 0.060: 54 0.060 - 0.080: 10 0.080 - 0.100: 9 Chirality restraints: 417 Sorted by residual: chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.52e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.48e-01 ... (remaining 414 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 952 " 0.003 2.00e-02 2.50e+03 6.56e-03 4.31e-01 pdb=" C VAL C 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL C 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN C 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " 0.003 2.00e-02 2.50e+03 6.38e-03 4.08e-01 pdb=" C VAL B 952 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL B 952 " 0.004 2.00e-02 2.50e+03 pdb=" N ASN B 953 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " -0.003 2.00e-02 2.50e+03 6.37e-03 4.06e-01 pdb=" C VAL A 952 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL A 952 " -0.004 2.00e-02 2.50e+03 pdb=" N ASN A 953 " -0.004 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 874 2.89 - 3.39: 2738 3.39 - 3.90: 4194 3.90 - 4.40: 4448 4.40 - 4.90: 7655 Nonbonded interactions: 19909 Sorted by model distance: nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.389 3.120 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.458 3.040 nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.459 3.040 ... (remaining 19904 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 '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: 1.110 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.840 Find NCS groups from input model: 0.030 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:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 2454 Z= 0.239 Angle : 0.319 2.279 3309 Z= 0.199 Chirality : 0.032 0.100 417 Planarity : 0.002 0.007 435 Dihedral : 14.893 89.342 912 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.41), residues: 312 helix: 2.81 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -2.14 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 983 PHE 0.009 0.002 PHE C 970 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 2454) covalent geometry : angle 0.31919 ( 3309) hydrogen bonds : bond 0.07520 ( 235) hydrogen bonds : angle 2.62641 ( 696) *********************** 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 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.105 Fit side-chains REVERT: A 974 SER cc_start: 0.8081 (p) cc_final: 0.7389 (p) REVERT: A 978 ASN cc_start: 0.8215 (m-40) cc_final: 0.7828 (m110) REVERT: C 979 ASP cc_start: 0.7179 (m-30) cc_final: 0.6959 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1822 time to fit residues: 3.8132 Evaluate side-chains 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN E1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.130849 restraints weight = 2984.133| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.03 r_work: 0.3826 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2454 Z= 0.129 Angle : 0.266 2.278 3309 Z= 0.155 Chirality : 0.031 0.098 417 Planarity : 0.001 0.009 435 Dihedral : 2.891 9.197 324 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: 5.09 (0.43), residues: 312 helix: 4.47 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -1.54 (0.64), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E1185 PHE 0.008 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2454) covalent geometry : angle 0.26639 ( 3309) hydrogen bonds : bond 0.03212 ( 235) hydrogen bonds : angle 2.26891 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.099 Fit side-chains REVERT: A 974 SER cc_start: 0.8300 (p) cc_final: 0.7649 (p) REVERT: A 978 ASN cc_start: 0.8368 (m-40) cc_final: 0.8071 (m110) REVERT: C 979 ASP cc_start: 0.7614 (m-30) cc_final: 0.7393 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1871 time to fit residues: 3.5662 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.149949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.131926 restraints weight = 3009.497| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.02 r_work: 0.3828 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2454 Z= 0.124 Angle : 0.249 1.897 3309 Z= 0.146 Chirality : 0.031 0.102 417 Planarity : 0.001 0.006 435 Dihedral : 2.783 8.768 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % 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: 5.83 (0.43), residues: 312 helix: 4.99 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.24 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E1185 PHE 0.009 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2454) covalent geometry : angle 0.24864 ( 3309) hydrogen bonds : bond 0.03197 ( 235) hydrogen bonds : angle 2.15949 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.119 Fit side-chains REVERT: A 974 SER cc_start: 0.8310 (p) cc_final: 0.7640 (p) REVERT: A 978 ASN cc_start: 0.8354 (m-40) cc_final: 0.8079 (m110) REVERT: C 979 ASP cc_start: 0.7608 (m-30) cc_final: 0.7389 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1731 time to fit residues: 3.0737 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 overall best weight: 0.2074 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.151440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.133457 restraints weight = 2930.706| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.01 r_work: 0.3851 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2454 Z= 0.082 Angle : 0.222 1.991 3309 Z= 0.133 Chirality : 0.031 0.103 417 Planarity : 0.001 0.004 435 Dihedral : 2.569 8.150 324 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 4.96 % Favored : 94.68 % 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: 6.41 (0.42), residues: 312 helix: 5.41 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.13 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 983 PHE 0.007 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00164 ( 2454) covalent geometry : angle 0.22202 ( 3309) hydrogen bonds : bond 0.03044 ( 235) hydrogen bonds : angle 1.99032 ( 696) *********************** 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 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.097 Fit side-chains REVERT: A 974 SER cc_start: 0.8269 (p) cc_final: 0.7616 (p) REVERT: A 978 ASN cc_start: 0.8328 (m-40) cc_final: 0.8089 (m110) REVERT: C 979 ASP cc_start: 0.7570 (m-30) cc_final: 0.7352 (m-30) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1759 time to fit residues: 3.4881 Evaluate side-chains 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.144505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.125048 restraints weight = 2949.653| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.10 r_work: 0.3800 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2454 Z= 0.190 Angle : 0.289 2.388 3309 Z= 0.165 Chirality : 0.034 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.884 9.453 324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: 5.92 (0.42), residues: 312 helix: 5.02 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.10 (0.68), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E1185 PHE 0.010 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 2454) covalent geometry : angle 0.28916 ( 3309) hydrogen bonds : bond 0.03334 ( 235) hydrogen bonds : angle 2.27064 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.090 Fit side-chains REVERT: A 974 SER cc_start: 0.8240 (p) cc_final: 0.7493 (p) REVERT: A 978 ASN cc_start: 0.8226 (m-40) cc_final: 0.7949 (m110) REVERT: C 979 ASP cc_start: 0.7447 (m-30) cc_final: 0.7227 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1817 time to fit residues: 3.4001 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.149610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.131611 restraints weight = 2934.598| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.01 r_work: 0.3830 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.148 Angle : 0.261 2.114 3309 Z= 0.151 Chirality : 0.032 0.101 417 Planarity : 0.001 0.005 435 Dihedral : 2.803 9.016 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 4.26 % Favored : 95.04 % 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: 6.02 (0.42), residues: 312 helix: 5.08 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -1.01 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 983 PHE 0.009 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2454) covalent geometry : angle 0.26095 ( 3309) hydrogen bonds : bond 0.03210 ( 235) hydrogen bonds : angle 2.19118 ( 696) *********************** 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 19 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.096 Fit side-chains REVERT: A 974 SER cc_start: 0.8275 (p) cc_final: 0.7581 (p) REVERT: A 978 ASN cc_start: 0.8296 (m-40) cc_final: 0.8058 (m110) REVERT: C 979 ASP cc_start: 0.7592 (m-30) cc_final: 0.7372 (m-30) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.1537 time to fit residues: 2.8908 Evaluate side-chains 18 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.143805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.124501 restraints weight = 2903.692| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.08 r_work: 0.3793 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2454 Z= 0.208 Angle : 0.303 2.883 3309 Z= 0.172 Chirality : 0.034 0.102 417 Planarity : 0.001 0.005 435 Dihedral : 2.976 9.897 324 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.67 (0.42), residues: 312 helix: 4.82 (0.25), residues: 246 sheet: None (None), residues: 0 loop : -1.06 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.010 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 2454) covalent geometry : angle 0.30333 ( 3309) hydrogen bonds : bond 0.03369 ( 235) hydrogen bonds : angle 2.34888 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.075 Fit side-chains REVERT: A 978 ASN cc_start: 0.8198 (m-40) cc_final: 0.7964 (m110) REVERT: C 979 ASP cc_start: 0.7470 (m-30) cc_final: 0.7235 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1846 time to fit residues: 3.2598 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.149539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131654 restraints weight = 2963.684| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.00 r_work: 0.3826 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2454 Z= 0.123 Angle : 0.250 2.220 3309 Z= 0.146 Chirality : 0.032 0.100 417 Planarity : 0.001 0.004 435 Dihedral : 2.768 8.771 324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % 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: 6.13 (0.42), residues: 312 helix: 5.15 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.93 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.008 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2454) covalent geometry : angle 0.25035 ( 3309) hydrogen bonds : bond 0.03177 ( 235) hydrogen bonds : angle 2.16527 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.098 Fit side-chains REVERT: A 978 ASN cc_start: 0.8272 (m-40) cc_final: 0.8050 (m110) REVERT: C 979 ASP cc_start: 0.7585 (m-30) cc_final: 0.7358 (m-30) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1515 time to fit residues: 2.7139 Evaluate side-chains 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 975 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 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 = 0.4277 r_free = 0.4277 target = 0.148260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130237 restraints weight = 2968.672| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.01 r_work: 0.3809 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2454 Z= 0.185 Angle : 0.289 2.882 3309 Z= 0.165 Chirality : 0.033 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.908 9.495 324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % 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: 5.86 (0.42), residues: 312 helix: 4.94 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.97 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 983 PHE 0.010 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2454) covalent geometry : angle 0.28924 ( 3309) hydrogen bonds : bond 0.03322 ( 235) hydrogen bonds : angle 2.29139 ( 696) *********************** 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 17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.055 Fit side-chains REVERT: A 978 ASN cc_start: 0.8323 (m-40) cc_final: 0.8091 (m110) REVERT: C 979 ASP cc_start: 0.7654 (m-30) cc_final: 0.7420 (m-30) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.1466 time to fit residues: 2.5736 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.131277 restraints weight = 3006.633| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.04 r_work: 0.3819 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2454 Z= 0.137 Angle : 0.260 2.390 3309 Z= 0.151 Chirality : 0.032 0.100 417 Planarity : 0.001 0.005 435 Dihedral : 2.794 8.941 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 6.12 (0.42), residues: 312 helix: 5.13 (0.24), residues: 246 sheet: None (None), residues: 0 loop : -0.90 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E1185 PHE 0.009 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2454) covalent geometry : angle 0.26050 ( 3309) hydrogen bonds : bond 0.03222 ( 235) hydrogen bonds : angle 2.19313 ( 696) ********************** 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 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.090 Fit side-chains REVERT: A 978 ASN cc_start: 0.8288 (m-40) cc_final: 0.8072 (m110) REVERT: C 979 ASP cc_start: 0.7599 (m-30) cc_final: 0.7371 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1735 time to fit residues: 3.0718 Evaluate side-chains 16 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.0050 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.1692 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.151394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.133569 restraints weight = 2959.451| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.00 r_work: 0.3850 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 2454 Z= 0.076 Angle : 0.223 2.311 3309 Z= 0.133 Chirality : 0.031 0.104 417 Planarity : 0.001 0.004 435 Dihedral : 2.513 8.181 324 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 6.62 (0.42), residues: 312 helix: 5.58 (0.22), residues: 243 sheet: None (None), residues: 0 loop : -0.80 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 983 PHE 0.007 0.001 PHE A 940 Details of bonding type rmsd covalent geometry : bond 0.00147 ( 2454) covalent geometry : angle 0.22310 ( 3309) hydrogen bonds : bond 0.02999 ( 235) hydrogen bonds : angle 1.96112 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1009.21 seconds wall clock time: 17 minutes 54.69 seconds (1074.69 seconds total)