Starting phenix.real_space_refine on Sun Mar 10 15:10:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/03_2024/7vzf_32227.pdb" } resolution = 2.95 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= 0.002 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 1617 2.51 5 N 468 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Time building chain proxies: 1.90, per 1000 atoms: 0.72 Number of scatterers: 2628 At special positions: 0 Unit cell: (98.8, 100.88, 37.44, 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 534 8.00 N 468 7.00 C 1617 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 - 3.50 Amino acid : False - 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: 0.97 Conformation dependent library (CDL) restraints added in 496.7 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.689A pdb=" N VAL A 7 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 7 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 41 removed outlier: 7.107A pdb=" N GLY B 33 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 35 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 36 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 37 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C 33 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 35 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 36 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 37 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.605A pdb=" N SER A 102 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N SER B 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 104 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 102 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER C 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 104 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AB1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.538A pdb=" N ALA A 145 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY A 147 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE A 149 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ALA B 152 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ILE A 151 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 145 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY B 147 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY C 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE B 149 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ALA C 152 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE B 151 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 26 hydrogen bonds defined for protein. 78 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: 0.58 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 886 1.33 - 1.45: 282 1.45 - 1.57: 1481 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 2658 Sorted by residual: bond pdb=" CB ASN A 19 " pdb=" CG ASN A 19 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.74e+00 bond pdb=" CB ASN C 19 " pdb=" CG ASN C 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.61e+00 bond pdb=" CB ASN B 19 " pdb=" CG ASN B 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.60e+00 bond pdb=" CB VAL B 118 " pdb=" CG1 VAL B 118 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB VAL C 118 " pdb=" CG1 VAL C 118 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 ... (remaining 2653 not shown) Histogram of bond angle deviations from ideal: 102.35 - 108.66: 202 108.66 - 114.96: 1523 114.96 - 121.27: 1033 121.27 - 127.58: 797 127.58 - 133.88: 24 Bond angle restraints: 3579 Sorted by residual: angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 128.35 -12.05 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU C 42 " pdb=" CB LEU C 42 " pdb=" CG LEU C 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.17e+01 angle pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" C ASP A 124 " ideal model delta sigma weight residual 110.80 117.81 -7.01 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" C ASP C 124 " ideal model delta sigma weight residual 110.80 117.78 -6.98 2.13e+00 2.20e-01 1.07e+01 ... (remaining 3574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1326 15.91 - 31.83: 177 31.83 - 47.74: 39 47.74 - 63.66: 3 63.66 - 79.57: 9 Dihedral angle restraints: 1554 sinusoidal: 585 harmonic: 969 Sorted by residual: dihedral pdb=" CA ILE B 18 " pdb=" C ILE B 18 " pdb=" N ASN B 19 " pdb=" CA ASN B 19 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE C 18 " pdb=" C ILE C 18 " pdb=" N ASN C 19 " pdb=" CA ASN C 19 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 18 " pdb=" C ILE A 18 " pdb=" N ASN A 19 " pdb=" CA ASN A 19 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 1551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 251 0.045 - 0.091: 110 0.091 - 0.136: 35 0.136 - 0.181: 12 0.181 - 0.226: 3 Chirality restraints: 411 Sorted by residual: chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL C 118 " pdb=" CA VAL C 118 " pdb=" CG1 VAL C 118 " pdb=" CG2 VAL C 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 408 not shown) Planarity restraints: 474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE B 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE A 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.18e+00 pdb=" CG PHE C 20 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 20 " 0.002 2.00e-02 2.50e+03 ... (remaining 471 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 36 2.56 - 3.14: 2294 3.14 - 3.73: 3944 3.73 - 4.31: 5191 4.31 - 4.90: 9443 Nonbonded interactions: 20908 Sorted by model distance: nonbonded pdb=" ND2 ASN A 53 " pdb=" O VAL C 14 " model vdw 1.971 2.520 nonbonded pdb=" OG1 THR A 137 " pdb=" O THR B 137 " model vdw 2.129 2.440 nonbonded pdb=" OG1 THR B 137 " pdb=" O THR C 137 " model vdw 2.160 2.440 nonbonded pdb=" ND1 HIS A 46 " pdb=" OE1 GLU B 100 " model vdw 2.204 2.520 nonbonded pdb=" N SER A 142 " pdb=" OG SER B 142 " model vdw 2.208 2.520 ... (remaining 20903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.330 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: 6.460 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4319 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 : 0.009 0.051 2658 Z= 0.654 Angle : 1.063 12.048 3579 Z= 0.566 Chirality : 0.060 0.226 411 Planarity : 0.006 0.034 474 Dihedral : 16.233 79.572 942 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 38.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.50 % Favored : 73.50 % Rotamer: Outliers : 0.00 % Allowed : 19.50 % Favored : 80.50 % 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: -5.56 (0.29), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.22), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 32 HIS 0.009 0.003 HIS B 43 PHE 0.030 0.004 PHE A 20 ARG 0.002 0.000 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.5870 (ttm170) cc_final: 0.5295 (tpm170) REVERT: A 143 ARG cc_start: 0.5537 (ptt180) cc_final: 0.4431 (mmp-170) REVERT: C 116 THR cc_start: 0.5679 (m) cc_final: 0.5469 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.7605 time to fit residues: 87.0958 Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 15 GLN B 48 HIS C 15 GLN C 48 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2658 Z= 0.310 Angle : 0.889 8.759 3579 Z= 0.468 Chirality : 0.054 0.159 411 Planarity : 0.004 0.022 474 Dihedral : 7.274 24.555 363 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 15.25 % Allowed : 23.05 % Favored : 61.70 % 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: -5.00 (0.31), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 32 HIS 0.005 0.001 HIS C 48 PHE 0.019 0.004 PHE B 50 ARG 0.008 0.002 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 44 time to evaluate : 0.309 Fit side-chains REVERT: A 115 ARG cc_start: 0.5796 (ttm170) cc_final: 0.5387 (tpm170) REVERT: A 122 LYS cc_start: 0.4412 (OUTLIER) cc_final: 0.3948 (mttt) REVERT: A 143 ARG cc_start: 0.5814 (ptt180) cc_final: 0.3916 (mmp80) REVERT: B 8 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5992 (pp) REVERT: B 46 HIS cc_start: 0.5040 (m90) cc_final: 0.4382 (p-80) REVERT: B 88 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6197 (t) outliers start: 43 outliers final: 11 residues processed: 84 average time/residue: 0.7156 time to fit residues: 62.2790 Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 21 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 120 HIS C 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.8353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2658 Z= 0.215 Angle : 0.746 7.315 3579 Z= 0.386 Chirality : 0.049 0.158 411 Planarity : 0.003 0.014 474 Dihedral : 5.970 22.362 363 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 9.57 % Allowed : 32.62 % Favored : 57.80 % 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: -4.72 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.006 0.001 HIS A 48 PHE 0.012 0.002 PHE B 20 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 32 time to evaluate : 0.291 Fit side-chains REVERT: A 115 ARG cc_start: 0.6052 (ttm170) cc_final: 0.5463 (tpm170) REVERT: A 143 ARG cc_start: 0.5919 (ptt180) cc_final: 0.4003 (mmp80) REVERT: A 153 GLN cc_start: 0.7617 (pt0) cc_final: 0.7282 (pt0) REVERT: B 8 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6165 (pp) REVERT: C 9 LYS cc_start: 0.4866 (pptt) cc_final: 0.4518 (pptt) REVERT: C 52 ASP cc_start: 0.4380 (OUTLIER) cc_final: 0.4082 (m-30) outliers start: 27 outliers final: 10 residues processed: 53 average time/residue: 0.9184 time to fit residues: 50.2296 Evaluate side-chains 36 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 24 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.0020 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 overall best weight: 1.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 48 HIS B 48 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 1.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2658 Z= 0.309 Angle : 0.890 10.595 3579 Z= 0.460 Chirality : 0.055 0.168 411 Planarity : 0.003 0.015 474 Dihedral : 7.054 26.304 363 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 13.48 % Allowed : 30.85 % Favored : 55.67 % 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: -4.63 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 32 HIS 0.005 0.002 HIS B 48 PHE 0.030 0.005 PHE B 20 ARG 0.004 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 32 time to evaluate : 0.276 Fit side-chains REVERT: A 50 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.4713 (t80) REVERT: A 115 ARG cc_start: 0.6701 (ttm170) cc_final: 0.5635 (tpm170) REVERT: B 50 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5653 (t80) REVERT: C 8 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6996 (tm) REVERT: C 111 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7661 (m) REVERT: C 117 LEU cc_start: 0.3955 (tp) cc_final: 0.3634 (pt) REVERT: C 120 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6432 (m90) outliers start: 38 outliers final: 10 residues processed: 61 average time/residue: 0.6402 time to fit residues: 40.7342 Evaluate side-chains 39 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 1.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2658 Z= 0.270 Angle : 0.845 12.936 3579 Z= 0.419 Chirality : 0.051 0.168 411 Planarity : 0.003 0.018 474 Dihedral : 6.388 25.332 363 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 10.99 % Allowed : 31.56 % Favored : 57.45 % 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: -4.57 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.003 0.001 HIS A 120 PHE 0.022 0.003 PHE B 20 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 24 time to evaluate : 0.271 Fit side-chains REVERT: A 50 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.4733 (t80) REVERT: A 115 ARG cc_start: 0.6764 (ttm170) cc_final: 0.5723 (tpp-160) REVERT: B 50 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.6050 (t80) REVERT: C 18 ILE cc_start: 0.4943 (OUTLIER) cc_final: 0.4160 (mp) REVERT: C 40 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: C 120 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6557 (m90) outliers start: 31 outliers final: 17 residues processed: 49 average time/residue: 0.7342 time to fit residues: 37.4369 Evaluate side-chains 43 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 21 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 1.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2658 Z= 0.178 Angle : 0.762 11.371 3579 Z= 0.373 Chirality : 0.049 0.131 411 Planarity : 0.002 0.014 474 Dihedral : 5.804 21.777 363 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 8.87 % Allowed : 34.04 % Favored : 57.09 % 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: -4.50 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 32 HIS 0.004 0.001 HIS A 48 PHE 0.010 0.002 PHE B 20 ARG 0.001 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 26 time to evaluate : 0.296 Fit side-chains REVERT: A 115 ARG cc_start: 0.6702 (ttm170) cc_final: 0.5701 (tpp-160) REVERT: B 50 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5947 (t80) REVERT: C 40 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5441 (pm20) outliers start: 25 outliers final: 11 residues processed: 45 average time/residue: 0.6791 time to fit residues: 31.9392 Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 22 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 1.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2658 Z= 0.386 Angle : 0.938 11.414 3579 Z= 0.473 Chirality : 0.054 0.159 411 Planarity : 0.004 0.023 474 Dihedral : 6.875 23.977 363 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 11.35 % Allowed : 33.33 % Favored : 55.32 % 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: -4.55 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 32 HIS 0.005 0.001 HIS A 120 PHE 0.032 0.005 PHE C 20 ARG 0.004 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 29 time to evaluate : 0.303 Fit side-chains REVERT: A 50 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.4931 (t80) REVERT: A 115 ARG cc_start: 0.7135 (ttm170) cc_final: 0.5915 (tpm170) REVERT: A 144 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7133 (pt) REVERT: B 24 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: B 50 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6283 (t80) REVERT: C 8 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6971 (tm) REVERT: C 18 ILE cc_start: 0.5341 (OUTLIER) cc_final: 0.4582 (mt) REVERT: C 40 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5701 (pm20) outliers start: 32 outliers final: 19 residues processed: 53 average time/residue: 0.7040 time to fit residues: 38.8695 Evaluate side-chains 51 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 25 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 1.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2658 Z= 0.211 Angle : 0.789 8.790 3579 Z= 0.395 Chirality : 0.048 0.132 411 Planarity : 0.003 0.018 474 Dihedral : 6.012 21.955 363 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.52 % Favored : 83.48 % Rotamer: Outliers : 7.80 % Allowed : 38.65 % Favored : 53.55 % 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: -4.47 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 32 HIS 0.004 0.001 HIS A 48 PHE 0.011 0.002 PHE A 50 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 31 time to evaluate : 0.299 Fit side-chains REVERT: A 39 THR cc_start: 0.6635 (m) cc_final: 0.6394 (p) REVERT: A 50 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.4818 (t80) REVERT: A 115 ARG cc_start: 0.6978 (ttm170) cc_final: 0.5868 (tpp-160) REVERT: B 24 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6179 (tp30) REVERT: B 50 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6010 (t80) REVERT: C 8 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6939 (tm) outliers start: 22 outliers final: 10 residues processed: 49 average time/residue: 0.7716 time to fit residues: 39.4432 Evaluate side-chains 40 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 26 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 1.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2658 Z= 0.202 Angle : 0.775 8.526 3579 Z= 0.385 Chirality : 0.048 0.141 411 Planarity : 0.003 0.020 474 Dihedral : 5.629 20.642 363 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 6.38 % Allowed : 39.72 % Favored : 53.90 % 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: -4.36 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 32 HIS 0.004 0.001 HIS A 48 PHE 0.014 0.002 PHE B 20 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 26 time to evaluate : 0.310 Fit side-chains REVERT: A 50 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.4791 (t80) REVERT: A 115 ARG cc_start: 0.6994 (ttm170) cc_final: 0.5908 (tpp-160) REVERT: B 24 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: B 50 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6020 (t80) REVERT: C 8 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6859 (tm) REVERT: C 18 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.4209 (mp) outliers start: 18 outliers final: 9 residues processed: 41 average time/residue: 0.7335 time to fit residues: 31.4299 Evaluate side-chains 36 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 22 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 1.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2658 Z= 0.268 Angle : 0.845 10.673 3579 Z= 0.421 Chirality : 0.050 0.147 411 Planarity : 0.003 0.024 474 Dihedral : 6.090 20.867 363 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 5.67 % Allowed : 41.13 % Favored : 53.19 % 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: -4.33 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.005 0.001 HIS A 120 PHE 0.022 0.003 PHE B 20 ARG 0.003 0.001 ARG A 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 23 time to evaluate : 0.351 Fit side-chains REVERT: A 50 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5060 (t80) REVERT: A 115 ARG cc_start: 0.7115 (ttm170) cc_final: 0.5999 (tpp-160) REVERT: B 24 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: B 50 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6217 (t80) REVERT: C 8 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7047 (tm) REVERT: C 18 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.4555 (mt) outliers start: 16 outliers final: 9 residues processed: 37 average time/residue: 0.9252 time to fit residues: 35.7068 Evaluate side-chains 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 19 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0010 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** 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 = 0.4848 r_free = 0.4848 target = 0.198182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.181543 restraints weight = 5249.558| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 2.77 r_work: 0.4580 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 1.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2658 Z= 0.273 Angle : 0.848 11.264 3579 Z= 0.423 Chirality : 0.049 0.154 411 Planarity : 0.003 0.019 474 Dihedral : 6.184 21.348 363 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 5.67 % Allowed : 41.49 % Favored : 52.84 % 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 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 32 HIS 0.004 0.001 HIS A 120 PHE 0.020 0.003 PHE C 20 ARG 0.003 0.001 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.09 seconds wall clock time: 27 minutes 13.19 seconds (1633.19 seconds total)