Starting phenix.real_space_refine on Mon Feb 10 20:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf6_37200/02_2025/8kf6_37200.cif" } resolution = 3.7 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1419 2.51 5 N 369 2.21 5 O 378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 2.61, per 1000 atoms: 1.20 Number of scatterers: 2175 At special positions: 0 Unit cell: (64.74, 95.45, 38.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 378 8.00 N 369 7.00 C 1419 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: 0.48 Conformation dependent library (CDL) restraints added in 257.5 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.215A pdb=" N VAL A 18 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.817A pdb=" N VAL A 40 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'G' and resid 24 through 25 removed outlier: 6.856A pdb=" N VAL G 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL H 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 10 hydrogen bonds defined for protein. 30 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: 0.45 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 705 1.34 - 1.45: 300 1.45 - 1.57: 1185 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 2208 Sorted by residual: bond pdb=" CA PHE B 20 " pdb=" C PHE B 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.37e-01 bond pdb=" CA PHE C 20 " pdb=" C PHE C 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.04e-01 bond pdb=" CA PHE A 20 " pdb=" C PHE A 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.03e-01 bond pdb=" CA VAL I 36 " pdb=" C VAL I 36 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.01e-01 bond pdb=" CB VAL A 18 " pdb=" CG2 VAL A 18 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.63e-01 ... (remaining 2203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2425 0.83 - 1.66: 421 1.66 - 2.49: 94 2.49 - 3.32: 18 3.32 - 4.15: 6 Bond angle restraints: 2964 Sorted by residual: angle pdb=" N GLU H 22 " pdb=" CA GLU H 22 " pdb=" C GLU H 22 " ideal model delta sigma weight residual 114.56 110.65 3.91 1.27e+00 6.20e-01 9.50e+00 angle pdb=" N GLY F 25 " pdb=" CA GLY F 25 " pdb=" C GLY F 25 " ideal model delta sigma weight residual 112.73 115.89 -3.16 1.20e+00 6.94e-01 6.94e+00 angle pdb=" CA GLY I 37 " pdb=" C GLY I 37 " pdb=" O GLY I 37 " ideal model delta sigma weight residual 122.39 120.13 2.26 9.30e-01 1.16e+00 5.93e+00 angle pdb=" C VAL H 12 " pdb=" N HIS H 13 " pdb=" CA HIS H 13 " ideal model delta sigma weight residual 121.80 117.65 4.15 1.71e+00 3.42e-01 5.88e+00 angle pdb=" C VAL F 24 " pdb=" N GLY F 25 " pdb=" CA GLY F 25 " ideal model delta sigma weight residual 119.98 122.37 -2.39 1.11e+00 8.12e-01 4.63e+00 ... (remaining 2959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1089 16.41 - 32.82: 123 32.82 - 49.22: 10 49.22 - 65.63: 4 65.63 - 82.04: 4 Dihedral angle restraints: 1230 sinusoidal: 444 harmonic: 786 Sorted by residual: dihedral pdb=" CA PHE C 20 " pdb=" C PHE C 20 " pdb=" N ALA C 21 " pdb=" CA ALA C 21 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE A 20 " pdb=" C PHE A 20 " pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE B 20 " pdb=" C PHE B 20 " pdb=" N ALA B 21 " pdb=" CA ALA B 21 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 1227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 163 0.031 - 0.062: 100 0.062 - 0.093: 18 0.093 - 0.124: 53 0.124 - 0.154: 11 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA VAL C 12 " pdb=" N VAL C 12 " pdb=" C VAL C 12 " pdb=" CB VAL C 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL A 12 " pdb=" N VAL A 12 " pdb=" C VAL A 12 " pdb=" CB VAL A 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 342 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 20 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C PHE G 20 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE G 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA G 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 20 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C PHE H 20 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE H 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA H 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 20 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C PHE I 20 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE I 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA I 21 " 0.008 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 891 2.91 - 3.41: 1959 3.41 - 3.91: 3231 3.91 - 4.40: 3503 4.40 - 4.90: 6933 Nonbonded interactions: 16517 Sorted by model distance: nonbonded pdb=" NZ LYS I 16 " pdb=" OE2 GLU I 22 " model vdw 2.415 3.120 nonbonded pdb=" OG SER F 26 " pdb=" N ASN F 27 " model vdw 2.418 3.120 nonbonded pdb=" OG SER I 26 " pdb=" N ASN I 27 " model vdw 2.465 3.120 nonbonded pdb=" OG SER H 26 " pdb=" N ASN H 27 " model vdw 2.473 3.120 nonbonded pdb=" CE1 PHE B 20 " pdb=" CE2 PHE C 20 " model vdw 2.493 3.640 ... (remaining 16512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 42) selection = (chain 'B' and resid 12 through 42) selection = (chain 'C' and resid 12 through 42) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 12 through 42) selection = (chain 'H' and resid 12 through 42) selection = (chain 'I' and resid 12 through 42) } 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 group one per residue 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.180 Find NCS groups from input model: 0.110 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.004 0.028 2208 Z= 0.278 Angle : 0.697 4.146 2964 Z= 0.423 Chirality : 0.059 0.154 345 Planarity : 0.003 0.014 372 Dihedral : 14.133 82.040 738 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.74 (0.32), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.24), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.009 0.002 PHE G 20 TYR 0.004 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.231 Fit side-chains REVERT: F 22 GLU cc_start: 0.8574 (tp30) cc_final: 0.8367 (tp30) REVERT: I 15 GLN cc_start: 0.8750 (mp10) cc_final: 0.8473 (mp10) REVERT: B 15 GLN cc_start: 0.8911 (mp10) cc_final: 0.8463 (mp10) REVERT: C 15 GLN cc_start: 0.8738 (mp10) cc_final: 0.8394 (mp10) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1566 time to fit residues: 4.7275 Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS F 15 GLN A 13 HIS G 13 HIS H 13 HIS E 13 HIS E 15 GLN I 13 HIS B 13 HIS C 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.118447 restraints weight = 2191.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.121536 restraints weight = 1361.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.123512 restraints weight = 997.571| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2208 Z= 0.297 Angle : 0.678 6.764 2964 Z= 0.373 Chirality : 0.060 0.153 345 Planarity : 0.003 0.014 372 Dihedral : 6.107 26.726 294 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 2.28 % Allowed : 10.05 % Favored : 87.67 % 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: -5.29 (0.34), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.26), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 13 PHE 0.010 0.002 PHE A 19 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.205 Fit side-chains REVERT: I 15 GLN cc_start: 0.8689 (mp10) cc_final: 0.8452 (mp10) REVERT: B 15 GLN cc_start: 0.8885 (mp10) cc_final: 0.8608 (mp10) REVERT: C 22 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7855 (pt0) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1321 time to fit residues: 4.6784 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.127351 restraints weight = 2135.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.130514 restraints weight = 1309.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.132678 restraints weight = 968.735| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2208 Z= 0.163 Angle : 0.562 5.313 2964 Z= 0.312 Chirality : 0.057 0.137 345 Planarity : 0.002 0.015 372 Dihedral : 5.799 28.581 294 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 3.65 % Allowed : 9.59 % Favored : 86.76 % 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: -4.87 (0.35), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.27), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.010 0.001 PHE B 20 TYR 0.005 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.233 Fit side-chains REVERT: B 15 GLN cc_start: 0.8794 (mp10) cc_final: 0.8449 (mp10) REVERT: B 22 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: C 22 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6897 (pp20) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.1356 time to fit residues: 4.9604 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.156616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.114781 restraints weight = 2244.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.117657 restraints weight = 1393.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.119693 restraints weight = 1032.762| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 2208 Z= 0.374 Angle : 0.696 6.228 2964 Z= 0.388 Chirality : 0.061 0.157 345 Planarity : 0.003 0.014 372 Dihedral : 6.140 30.305 294 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.94 % Favored : 77.06 % Rotamer: Outliers : 3.20 % Allowed : 12.33 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.81 (0.36), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.28), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 13 PHE 0.016 0.003 PHE A 19 TYR 0.008 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.233 Fit side-chains REVERT: G 28 LYS cc_start: 0.8191 (mttt) cc_final: 0.7833 (mttp) REVERT: H 28 LYS cc_start: 0.8258 (mttt) cc_final: 0.7867 (mttp) REVERT: B 15 GLN cc_start: 0.8915 (mp10) cc_final: 0.8702 (mp10) REVERT: C 22 GLU cc_start: 0.8197 (pt0) cc_final: 0.7912 (pt0) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1638 time to fit residues: 6.7604 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.160975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.118649 restraints weight = 2122.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.121947 restraints weight = 1296.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.124064 restraints weight = 951.771| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2208 Z= 0.151 Angle : 0.533 5.043 2964 Z= 0.297 Chirality : 0.056 0.133 345 Planarity : 0.002 0.015 372 Dihedral : 5.657 27.942 294 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 3.65 % Allowed : 12.33 % Favored : 84.02 % 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: -4.34 (0.38), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.010 0.001 PHE B 20 TYR 0.004 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.222 Fit side-chains REVERT: E 35 MET cc_start: 0.8608 (tpp) cc_final: 0.8273 (tpp) REVERT: B 15 GLN cc_start: 0.8777 (mp10) cc_final: 0.8326 (mp10) REVERT: B 22 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6839 (pp20) REVERT: C 22 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6947 (pp20) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.1191 time to fit residues: 4.4430 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.112708 restraints weight = 2255.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.115313 restraints weight = 1435.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.116958 restraints weight = 1083.139| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2208 Z= 0.312 Angle : 0.630 5.786 2964 Z= 0.354 Chirality : 0.059 0.157 345 Planarity : 0.003 0.016 372 Dihedral : 5.876 29.438 294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.79 % Favored : 79.21 % Rotamer: Outliers : 3.65 % Allowed : 14.16 % Favored : 82.19 % 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: -4.35 (0.39), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.019 0.002 PHE H 20 TYR 0.008 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.216 Fit side-chains REVERT: F 35 MET cc_start: 0.8387 (ttp) cc_final: 0.8154 (ttp) REVERT: G 28 LYS cc_start: 0.8153 (mttt) cc_final: 0.7809 (mttp) REVERT: H 28 LYS cc_start: 0.8299 (mttt) cc_final: 0.7931 (mttm) REVERT: B 15 GLN cc_start: 0.8829 (mp10) cc_final: 0.8564 (mp10) REVERT: B 22 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: C 22 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6853 (pp20) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.1536 time to fit residues: 5.9648 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.151569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.109257 restraints weight = 2223.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.112446 restraints weight = 1345.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.114478 restraints weight = 983.915| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2208 Z= 0.289 Angle : 0.616 5.750 2964 Z= 0.346 Chirality : 0.059 0.154 345 Planarity : 0.003 0.015 372 Dihedral : 5.879 28.987 294 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.56 % Favored : 82.44 % Rotamer: Outliers : 4.11 % Allowed : 13.70 % Favored : 82.19 % 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: -4.26 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.020 0.002 PHE H 20 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.237 Fit side-chains REVERT: F 35 MET cc_start: 0.8621 (ttp) cc_final: 0.8420 (ttp) REVERT: D 22 GLU cc_start: 0.8537 (tp30) cc_final: 0.7835 (mp0) REVERT: D 35 MET cc_start: 0.8818 (mmm) cc_final: 0.8154 (ttm) REVERT: B 15 GLN cc_start: 0.8852 (mp10) cc_final: 0.8486 (mp10) REVERT: B 22 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: C 22 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6874 (pp20) outliers start: 9 outliers final: 7 residues processed: 32 average time/residue: 0.1255 time to fit residues: 4.9764 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.159473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.116686 restraints weight = 2179.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.120003 restraints weight = 1310.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.122229 restraints weight = 956.881| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2208 Z= 0.157 Angle : 0.519 5.098 2964 Z= 0.291 Chirality : 0.056 0.142 345 Planarity : 0.002 0.015 372 Dihedral : 5.497 27.310 294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.11 % Allowed : 14.61 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.42), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.010 0.001 PHE B 20 TYR 0.004 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.223 Fit side-chains REVERT: A 22 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6771 (pp20) REVERT: D 22 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: D 35 MET cc_start: 0.8762 (mmm) cc_final: 0.8105 (ttm) REVERT: E 35 MET cc_start: 0.8608 (tpp) cc_final: 0.8288 (tpp) REVERT: B 15 GLN cc_start: 0.8741 (mp10) cc_final: 0.8402 (mp10) REVERT: B 22 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6785 (pp20) REVERT: C 22 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6917 (pp20) outliers start: 9 outliers final: 5 residues processed: 30 average time/residue: 0.1075 time to fit residues: 4.0942 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.152402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.111561 restraints weight = 2318.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.114312 restraints weight = 1459.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.116154 restraints weight = 1089.609| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2208 Z= 0.339 Angle : 0.635 5.865 2964 Z= 0.358 Chirality : 0.060 0.156 345 Planarity : 0.003 0.015 372 Dihedral : 5.869 28.726 294 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 4.57 % Allowed : 14.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.42), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.015 0.002 PHE C 19 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.255 Fit side-chains REVERT: G 28 LYS cc_start: 0.8065 (mttt) cc_final: 0.7677 (mttp) REVERT: D 22 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: D 35 MET cc_start: 0.8734 (mmm) cc_final: 0.8206 (ttm) REVERT: H 28 LYS cc_start: 0.8209 (mttt) cc_final: 0.7812 (mttp) REVERT: E 35 MET cc_start: 0.8745 (tpp) cc_final: 0.8410 (tpp) REVERT: B 15 GLN cc_start: 0.8859 (mp10) cc_final: 0.8563 (mp10) REVERT: B 22 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: C 22 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6869 (pp20) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.1465 time to fit residues: 5.9891 Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.156331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.114190 restraints weight = 2153.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.117055 restraints weight = 1328.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.119098 restraints weight = 990.161| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2208 Z= 0.191 Angle : 0.543 5.285 2964 Z= 0.304 Chirality : 0.057 0.144 345 Planarity : 0.002 0.015 372 Dihedral : 5.620 27.554 294 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.11 % Allowed : 14.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.43), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.011 0.001 PHE B 20 TYR 0.005 0.001 TYR H 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.235 Fit side-chains REVERT: F 28 LYS cc_start: 0.8585 (mttm) cc_final: 0.8354 (mttm) REVERT: D 22 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: D 35 MET cc_start: 0.8753 (mmm) cc_final: 0.8032 (ttm) REVERT: E 35 MET cc_start: 0.8706 (tpp) cc_final: 0.8346 (tpp) REVERT: B 15 GLN cc_start: 0.8782 (mp10) cc_final: 0.8434 (mp10) REVERT: B 22 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: C 22 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6802 (pp20) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.1216 time to fit residues: 4.6941 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.149192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106683 restraints weight = 2255.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.109685 restraints weight = 1382.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.111738 restraints weight = 1023.698| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2208 Z= 0.352 Angle : 0.651 5.827 2964 Z= 0.366 Chirality : 0.060 0.158 345 Planarity : 0.003 0.019 372 Dihedral : 5.898 28.591 294 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % Rotamer: Outliers : 4.11 % Allowed : 14.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.43), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.015 0.003 PHE A 19 TYR 0.008 0.001 TYR H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1072.55 seconds wall clock time: 19 minutes 54.82 seconds (1194.82 seconds total)