Starting phenix.real_space_refine on Sun Mar 10 17:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/03_2024/8gvk_32099.pdb" } resolution = 2.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 53": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "D ARG 53": "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: 3567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.27, per 1000 atoms: 0.64 Number of scatterers: 3567 At special positions: 0 Unit cell: (68.0021, 57.6201, 62.8111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 723 8.00 N 620 7.00 C 2224 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: 1.20 Conformation dependent library (CDL) restraints added in 626.7 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 3.4% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.334A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 516 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: 0.93 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.37: 640 1.37 - 1.44: 524 1.44 - 1.51: 770 1.51 - 1.58: 1130 Bond restraints: 3636 Sorted by residual: bond pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.79e+00 bond pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.75e+00 bond pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.56e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 102.98 - 109.19: 459 109.19 - 115.41: 1808 115.41 - 121.62: 1650 121.62 - 127.84: 995 127.84 - 134.05: 64 Bond angle restraints: 4976 Sorted by residual: angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 125.96 -11.86 2.00e+00 2.50e-01 3.52e+01 angle pdb=" CA GLU C 101 " pdb=" CB GLU C 101 " pdb=" CG GLU C 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU B 101 " pdb=" CB GLU B 101 " pdb=" CG GLU B 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 125.90 -11.80 2.00e+00 2.50e-01 3.48e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 131.28 -9.31 1.80e+00 3.09e-01 2.68e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1776 16.70 - 33.41: 148 33.41 - 50.11: 44 50.11 - 66.82: 8 66.82 - 83.52: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual 180.00 -103.09 -76.91 0 5.00e+00 4.00e-02 2.37e+02 dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 -103.12 -76.88 0 5.00e+00 4.00e-02 2.36e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual -180.00 -103.15 -76.85 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 340 0.046 - 0.093: 159 0.093 - 0.139: 41 0.139 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CB ILE B 17 " pdb=" CA ILE B 17 " pdb=" CG1 ILE B 17 " pdb=" CG2 ILE B 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE D 17 " pdb=" CA ILE D 17 " pdb=" CG1 ILE D 17 " pdb=" CG2 ILE D 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 17 " pdb=" CA ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CG2 ILE A 17 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU B 101 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 101 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C GLU D 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU D 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA D 102 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 101 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C GLU A 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 76 2.63 - 3.19: 2732 3.19 - 3.76: 6021 3.76 - 4.33: 8262 4.33 - 4.90: 13553 Nonbonded interactions: 30644 Sorted by model distance: nonbonded pdb=" O SER D 69 " pdb=" O HOH D 201 " model vdw 2.057 2.440 nonbonded pdb=" O SER B 69 " pdb=" O HOH B 201 " model vdw 2.178 2.440 nonbonded pdb=" O SER A 69 " pdb=" O HOH A 201 " model vdw 2.219 2.440 nonbonded pdb=" OE2 GLU B 44 " pdb=" NH1 ARG B 53 " model vdw 2.228 2.520 nonbonded pdb=" O SER C 69 " pdb=" O HOH C 201 " model vdw 2.251 2.440 ... (remaining 30639 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.810 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 3636 Z= 0.424 Angle : 1.289 11.858 4976 Z= 0.716 Chirality : 0.059 0.231 556 Planarity : 0.005 0.026 624 Dihedral : 15.347 83.520 1160 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 2.56 % Allowed : 3.42 % Favored : 94.02 % Rotamer: Outliers : 4.07 % Allowed : 5.23 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.66 (0.27), residues: 264 loop : -1.39 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 108 HIS 0.001 0.000 HIS C 87 PHE 0.011 0.002 PHE C 29 TYR 0.010 0.002 TYR A 96 ARG 0.002 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.380 Fit side-chains REVERT: A 52 SER cc_start: 0.6298 (m) cc_final: 0.5932 (m) REVERT: A 103 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6694 (ttp80) REVERT: A 116 GLU cc_start: 0.6511 (tp30) cc_final: 0.6193 (tm-30) REVERT: A 121 LYS cc_start: 0.7918 (pttt) cc_final: 0.7712 (pttm) REVERT: B 103 ARG cc_start: 0.7139 (tpp-160) cc_final: 0.6742 (ttp80) REVERT: B 116 GLU cc_start: 0.6584 (tp30) cc_final: 0.6301 (tm-30) REVERT: B 121 LYS cc_start: 0.7890 (pttt) cc_final: 0.7644 (pttm) REVERT: C 53 ARG cc_start: 0.6940 (mtt90) cc_final: 0.6548 (mtt-85) REVERT: C 103 ARG cc_start: 0.7130 (tpp-160) cc_final: 0.6711 (ttp80) REVERT: C 116 GLU cc_start: 0.6554 (tp30) cc_final: 0.6307 (tm-30) REVERT: C 121 LYS cc_start: 0.7915 (pttt) cc_final: 0.7677 (pttm) REVERT: D 52 SER cc_start: 0.5883 (m) cc_final: 0.5565 (m) REVERT: D 103 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6749 (ttp80) REVERT: D 121 LYS cc_start: 0.7906 (pttt) cc_final: 0.7668 (pttm) outliers start: 14 outliers final: 0 residues processed: 71 average time/residue: 1.3046 time to fit residues: 95.2209 Evaluate side-chains 43 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN B 107 GLN B 118 ASN B 127 HIS C 107 GLN C 118 ASN C 127 HIS D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3636 Z= 0.313 Angle : 0.890 7.367 4976 Z= 0.478 Chirality : 0.049 0.175 556 Planarity : 0.004 0.030 624 Dihedral : 9.134 62.025 512 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 2.56 % Allowed : 4.06 % Favored : 93.38 % Rotamer: Outliers : 5.52 % Allowed : 9.59 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -0.62 (0.34), residues: 468 helix: None (None), residues: 0 sheet: 0.02 (0.25), residues: 284 loop : -0.98 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 79 HIS 0.002 0.001 HIS B 87 PHE 0.014 0.003 PHE A 29 TYR 0.009 0.002 TYR D 83 ARG 0.004 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.390 Fit side-chains REVERT: A 52 SER cc_start: 0.6253 (m) cc_final: 0.5961 (m) REVERT: A 53 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6591 (mtt-85) REVERT: A 103 ARG cc_start: 0.7123 (tpp-160) cc_final: 0.6684 (ttp80) REVERT: A 121 LYS cc_start: 0.7885 (pttt) cc_final: 0.7634 (pttp) REVERT: B 52 SER cc_start: 0.6143 (OUTLIER) cc_final: 0.5792 (m) REVERT: B 53 ARG cc_start: 0.7025 (ttm110) cc_final: 0.6546 (mtt-85) REVERT: B 103 ARG cc_start: 0.7107 (tpp-160) cc_final: 0.6690 (ttp80) REVERT: B 121 LYS cc_start: 0.7890 (pttt) cc_final: 0.7634 (pttp) REVERT: C 52 SER cc_start: 0.6178 (OUTLIER) cc_final: 0.5825 (m) REVERT: C 53 ARG cc_start: 0.7049 (mtt90) cc_final: 0.6463 (mtm-85) REVERT: C 103 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6675 (ttp80) REVERT: C 121 LYS cc_start: 0.7894 (pttt) cc_final: 0.7644 (pttp) REVERT: D 52 SER cc_start: 0.6193 (m) cc_final: 0.5911 (m) REVERT: D 53 ARG cc_start: 0.7051 (ttm110) cc_final: 0.6519 (mtt-85) REVERT: D 103 ARG cc_start: 0.7104 (tpp-160) cc_final: 0.6688 (ttp80) REVERT: D 121 LYS cc_start: 0.7872 (pttt) cc_final: 0.7615 (pttp) outliers start: 19 outliers final: 10 residues processed: 66 average time/residue: 1.3451 time to fit residues: 91.2558 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3636 Z= 0.384 Angle : 0.935 7.780 4976 Z= 0.501 Chirality : 0.052 0.187 556 Planarity : 0.005 0.038 624 Dihedral : 8.886 57.317 512 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer: Outliers : 4.65 % Allowed : 16.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.33), residues: 468 helix: -4.52 (0.34), residues: 24 sheet: 0.24 (0.26), residues: 284 loop : -2.05 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP D 79 HIS 0.002 0.001 HIS C 87 PHE 0.014 0.003 PHE A 29 TYR 0.008 0.002 TYR C 96 ARG 0.003 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.399 Fit side-chains REVERT: A 52 SER cc_start: 0.6314 (m) cc_final: 0.6062 (m) REVERT: A 103 ARG cc_start: 0.7105 (tpp-160) cc_final: 0.6654 (ttm170) REVERT: A 121 LYS cc_start: 0.7855 (pttt) cc_final: 0.7624 (pttp) REVERT: B 52 SER cc_start: 0.6311 (OUTLIER) cc_final: 0.5731 (m) REVERT: B 103 ARG cc_start: 0.7108 (tpp-160) cc_final: 0.6667 (ttm170) REVERT: B 121 LYS cc_start: 0.7850 (pttt) cc_final: 0.7616 (pttp) REVERT: C 52 SER cc_start: 0.6188 (OUTLIER) cc_final: 0.5573 (m) REVERT: C 53 ARG cc_start: 0.7041 (mtt90) cc_final: 0.6557 (mtt-85) REVERT: C 103 ARG cc_start: 0.7102 (tpp-160) cc_final: 0.6655 (ttm170) REVERT: C 121 LYS cc_start: 0.7856 (pttt) cc_final: 0.7625 (pttp) REVERT: D 52 SER cc_start: 0.6335 (m) cc_final: 0.6106 (m) REVERT: D 103 ARG cc_start: 0.7102 (tpp-160) cc_final: 0.6660 (ttm170) REVERT: D 121 LYS cc_start: 0.7843 (pttt) cc_final: 0.7605 (pttp) outliers start: 16 outliers final: 8 residues processed: 62 average time/residue: 1.2473 time to fit residues: 79.7296 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3636 Z= 0.295 Angle : 0.851 7.466 4976 Z= 0.449 Chirality : 0.048 0.183 556 Planarity : 0.004 0.038 624 Dihedral : 8.207 50.595 512 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 4.65 % Allowed : 16.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.96 (0.34), residues: 468 helix: -4.39 (0.39), residues: 24 sheet: 0.33 (0.25), residues: 288 loop : -1.79 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 79 HIS 0.001 0.001 HIS C 87 PHE 0.012 0.003 PHE A 29 TYR 0.010 0.002 TYR C 96 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.388 Fit side-chains REVERT: A 52 SER cc_start: 0.6296 (m) cc_final: 0.6061 (m) REVERT: A 103 ARG cc_start: 0.7083 (tpp-160) cc_final: 0.6609 (ttp80) REVERT: A 121 LYS cc_start: 0.7848 (pttt) cc_final: 0.7591 (pttp) REVERT: B 52 SER cc_start: 0.6332 (OUTLIER) cc_final: 0.5987 (m) REVERT: B 103 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6623 (ttp80) REVERT: B 121 LYS cc_start: 0.7845 (pttt) cc_final: 0.7584 (pttp) REVERT: C 52 SER cc_start: 0.6196 (OUTLIER) cc_final: 0.5570 (m) REVERT: C 53 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6565 (mtt-85) REVERT: C 103 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6607 (ttp80) REVERT: C 121 LYS cc_start: 0.7847 (pttt) cc_final: 0.7589 (pttp) REVERT: D 52 SER cc_start: 0.6324 (m) cc_final: 0.6094 (m) REVERT: D 103 ARG cc_start: 0.7070 (tpp-160) cc_final: 0.6602 (ttp80) REVERT: D 121 LYS cc_start: 0.7832 (pttt) cc_final: 0.7572 (pttp) outliers start: 16 outliers final: 9 residues processed: 54 average time/residue: 1.2782 time to fit residues: 71.1132 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3636 Z= 0.406 Angle : 0.914 7.882 4976 Z= 0.485 Chirality : 0.051 0.173 556 Planarity : 0.005 0.039 624 Dihedral : 8.214 45.538 512 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 5.52 % Allowed : 15.70 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.33), residues: 468 helix: -4.32 (0.42), residues: 24 sheet: 0.24 (0.25), residues: 288 loop : -1.93 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP D 120 HIS 0.002 0.001 HIS C 87 PHE 0.014 0.004 PHE A 29 TYR 0.010 0.002 TYR C 96 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 0.368 Fit side-chains REVERT: A 52 SER cc_start: 0.6331 (m) cc_final: 0.6111 (m) REVERT: A 103 ARG cc_start: 0.7122 (tpp-160) cc_final: 0.6641 (ttp80) REVERT: A 121 LYS cc_start: 0.7847 (pttt) cc_final: 0.7622 (pttp) REVERT: B 52 SER cc_start: 0.6332 (OUTLIER) cc_final: 0.5984 (m) REVERT: B 103 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6648 (ttp80) REVERT: B 121 LYS cc_start: 0.7838 (pttt) cc_final: 0.7611 (pttp) REVERT: C 52 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5505 (m) REVERT: C 53 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6543 (mtt-85) REVERT: C 103 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6629 (ttp80) REVERT: C 121 LYS cc_start: 0.7842 (pttt) cc_final: 0.7617 (pttp) REVERT: D 103 ARG cc_start: 0.7115 (tpp-160) cc_final: 0.6644 (ttp80) REVERT: D 121 LYS cc_start: 0.7822 (pttt) cc_final: 0.7597 (pttp) outliers start: 19 outliers final: 9 residues processed: 57 average time/residue: 1.2594 time to fit residues: 73.9909 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.211 Angle : 0.777 7.280 4976 Z= 0.409 Chirality : 0.046 0.153 556 Planarity : 0.003 0.025 624 Dihedral : 7.283 38.505 512 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 1.71 % Allowed : 3.42 % Favored : 94.87 % Rotamer: Outliers : 4.36 % Allowed : 16.28 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 468 helix: -4.36 (0.40), residues: 24 sheet: 0.15 (0.25), residues: 296 loop : -1.57 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 108 HIS 0.001 0.001 HIS C 87 PHE 0.010 0.003 PHE A 29 TYR 0.011 0.001 TYR A 96 ARG 0.001 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.433 Fit side-chains REVERT: A 103 ARG cc_start: 0.7008 (tpp-160) cc_final: 0.6693 (ttp80) REVERT: A 121 LYS cc_start: 0.7833 (pttt) cc_final: 0.7597 (pttp) REVERT: B 52 SER cc_start: 0.6333 (OUTLIER) cc_final: 0.5986 (m) REVERT: B 103 ARG cc_start: 0.7010 (tpp-160) cc_final: 0.6697 (ttp80) REVERT: B 121 LYS cc_start: 0.7825 (pttt) cc_final: 0.7584 (pttp) REVERT: C 52 SER cc_start: 0.6166 (OUTLIER) cc_final: 0.5534 (m) REVERT: C 53 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6577 (mtt-85) REVERT: C 103 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6682 (ttp80) REVERT: C 121 LYS cc_start: 0.7831 (pttt) cc_final: 0.7593 (pttp) REVERT: D 103 ARG cc_start: 0.7011 (tpp-160) cc_final: 0.6694 (ttp80) REVERT: D 121 LYS cc_start: 0.7815 (pttt) cc_final: 0.7575 (pttp) outliers start: 15 outliers final: 5 residues processed: 53 average time/residue: 1.3805 time to fit residues: 75.3765 Evaluate side-chains 51 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 overall best weight: 1.7762 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3636 Z= 0.170 Angle : 0.716 6.393 4976 Z= 0.379 Chirality : 0.044 0.147 556 Planarity : 0.003 0.018 624 Dihedral : 6.487 27.204 512 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.42 % Favored : 95.73 % Rotamer: Outliers : 4.36 % Allowed : 17.44 % Favored : 78.20 % 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: -0.89 (0.35), residues: 468 helix: -4.65 (0.28), residues: 24 sheet: 0.21 (0.26), residues: 296 loop : -1.40 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 108 HIS 0.001 0.000 HIS A 127 PHE 0.009 0.002 PHE A 29 TYR 0.011 0.001 TYR A 96 ARG 0.001 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.389 Fit side-chains REVERT: A 88 SER cc_start: 0.8807 (p) cc_final: 0.8443 (m) REVERT: A 103 ARG cc_start: 0.6973 (tpp-160) cc_final: 0.6690 (ttp80) REVERT: A 121 LYS cc_start: 0.7840 (pttt) cc_final: 0.7582 (pttp) REVERT: B 88 SER cc_start: 0.8814 (p) cc_final: 0.8450 (m) REVERT: B 103 ARG cc_start: 0.6975 (tpp-160) cc_final: 0.6700 (ttp80) REVERT: B 121 LYS cc_start: 0.7834 (pttt) cc_final: 0.7571 (pttp) REVERT: C 52 SER cc_start: 0.6256 (OUTLIER) cc_final: 0.5890 (m) REVERT: C 53 ARG cc_start: 0.7010 (mtt90) cc_final: 0.6489 (mtm-85) REVERT: C 88 SER cc_start: 0.8817 (p) cc_final: 0.8469 (m) REVERT: C 103 ARG cc_start: 0.6968 (tpp-160) cc_final: 0.6681 (ttp80) REVERT: C 121 LYS cc_start: 0.7836 (pttt) cc_final: 0.7578 (pttp) REVERT: D 88 SER cc_start: 0.8820 (p) cc_final: 0.8467 (m) REVERT: D 103 ARG cc_start: 0.6978 (tpp-160) cc_final: 0.6698 (ttp80) REVERT: D 121 LYS cc_start: 0.7823 (pttt) cc_final: 0.7559 (pttp) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 1.0604 time to fit residues: 74.6561 Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3636 Z= 0.319 Angle : 0.813 7.402 4976 Z= 0.436 Chirality : 0.048 0.151 556 Planarity : 0.004 0.033 624 Dihedral : 7.054 24.865 512 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 4.36 % Allowed : 16.57 % Favored : 79.07 % 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: -0.93 (0.33), residues: 468 helix: -4.35 (0.41), residues: 24 sheet: 0.33 (0.25), residues: 288 loop : -1.75 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 120 HIS 0.002 0.001 HIS C 87 PHE 0.012 0.003 PHE D 29 TYR 0.010 0.002 TYR A 96 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.385 Fit side-chains REVERT: A 103 ARG cc_start: 0.7053 (tpp-160) cc_final: 0.6706 (ttp80) REVERT: A 121 LYS cc_start: 0.7829 (pttt) cc_final: 0.7584 (pttp) REVERT: B 52 SER cc_start: 0.6397 (OUTLIER) cc_final: 0.6043 (m) REVERT: B 103 ARG cc_start: 0.7052 (tpp-160) cc_final: 0.6712 (ttp80) REVERT: B 121 LYS cc_start: 0.7821 (pttt) cc_final: 0.7570 (pttp) REVERT: C 52 SER cc_start: 0.6209 (OUTLIER) cc_final: 0.5571 (m) REVERT: C 53 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6598 (mtt-85) REVERT: C 103 ARG cc_start: 0.7050 (tpp-160) cc_final: 0.6701 (ttp80) REVERT: C 121 LYS cc_start: 0.7828 (pttt) cc_final: 0.7597 (pttp) REVERT: D 103 ARG cc_start: 0.7050 (tpp-160) cc_final: 0.6706 (ttp80) REVERT: D 121 LYS cc_start: 0.7811 (pttt) cc_final: 0.7562 (pttp) outliers start: 15 outliers final: 7 residues processed: 53 average time/residue: 1.3684 time to fit residues: 74.6445 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3636 Z= 0.175 Angle : 0.701 6.591 4976 Z= 0.377 Chirality : 0.044 0.138 556 Planarity : 0.003 0.019 624 Dihedral : 6.517 24.345 512 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 1.74 % Allowed : 19.19 % Favored : 79.07 % 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: -0.95 (0.35), residues: 468 helix: -4.62 (0.30), residues: 24 sheet: 0.18 (0.26), residues: 296 loop : -1.44 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 108 HIS 0.001 0.000 HIS C 87 PHE 0.008 0.002 PHE D 29 TYR 0.011 0.001 TYR A 96 ARG 0.004 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.409 Fit side-chains REVERT: A 88 SER cc_start: 0.8822 (p) cc_final: 0.8444 (m) REVERT: A 103 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.6693 (ttp80) REVERT: A 121 LYS cc_start: 0.7826 (pttt) cc_final: 0.7585 (pttp) REVERT: B 52 SER cc_start: 0.6365 (OUTLIER) cc_final: 0.6009 (m) REVERT: B 88 SER cc_start: 0.8826 (p) cc_final: 0.8447 (m) REVERT: B 103 ARG cc_start: 0.6967 (tpp-160) cc_final: 0.6695 (ttp80) REVERT: B 121 LYS cc_start: 0.7820 (pttt) cc_final: 0.7574 (pttp) REVERT: C 52 SER cc_start: 0.6285 (OUTLIER) cc_final: 0.5682 (m) REVERT: C 53 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6516 (mtm-85) REVERT: C 88 SER cc_start: 0.8823 (p) cc_final: 0.8460 (m) REVERT: C 103 ARG cc_start: 0.6967 (tpp-160) cc_final: 0.6685 (ttp80) REVERT: C 121 LYS cc_start: 0.7822 (pttt) cc_final: 0.7581 (pttp) REVERT: D 88 SER cc_start: 0.8835 (p) cc_final: 0.8461 (m) REVERT: D 103 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.6691 (ttp80) REVERT: D 121 LYS cc_start: 0.7804 (pttt) cc_final: 0.7561 (pttp) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 1.4028 time to fit residues: 75.0377 Evaluate side-chains 52 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.194 Angle : 0.714 6.776 4976 Z= 0.384 Chirality : 0.045 0.136 556 Planarity : 0.003 0.021 624 Dihedral : 6.564 25.170 512 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 1.16 % Allowed : 19.77 % Favored : 79.07 % 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: -0.94 (0.35), residues: 468 helix: -4.66 (0.28), residues: 24 sheet: 0.21 (0.26), residues: 296 loop : -1.51 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 108 HIS 0.001 0.000 HIS D 87 PHE 0.008 0.002 PHE D 29 TYR 0.011 0.001 TYR D 22 ARG 0.003 0.000 ARG A 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.383 Fit side-chains REVERT: A 88 SER cc_start: 0.8818 (p) cc_final: 0.8433 (m) REVERT: A 103 ARG cc_start: 0.6998 (tpp-160) cc_final: 0.6718 (ttp80) REVERT: A 121 LYS cc_start: 0.7824 (pttt) cc_final: 0.7589 (pttp) REVERT: B 52 SER cc_start: 0.6356 (OUTLIER) cc_final: 0.5992 (m) REVERT: B 88 SER cc_start: 0.8821 (p) cc_final: 0.8441 (m) REVERT: B 103 ARG cc_start: 0.6996 (tpp-160) cc_final: 0.6718 (ttp80) REVERT: B 121 LYS cc_start: 0.7816 (pttt) cc_final: 0.7576 (pttp) REVERT: C 52 SER cc_start: 0.6268 (m) cc_final: 0.5894 (m) REVERT: C 53 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6537 (mtm-85) REVERT: C 88 SER cc_start: 0.8818 (p) cc_final: 0.8445 (m) REVERT: C 103 ARG cc_start: 0.6994 (tpp-160) cc_final: 0.6708 (ttp80) REVERT: C 121 LYS cc_start: 0.7819 (pttt) cc_final: 0.7583 (pttp) REVERT: D 88 SER cc_start: 0.8824 (p) cc_final: 0.8451 (m) REVERT: D 103 ARG cc_start: 0.6990 (tpp-160) cc_final: 0.6703 (ttp80) REVERT: D 121 LYS cc_start: 0.7803 (pttt) cc_final: 0.7564 (pttp) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 1.3071 time to fit residues: 72.7026 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 0.0070 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.170559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140205 restraints weight = 3036.974| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.39 r_work: 0.3465 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3636 Z= 0.203 Angle : 0.724 6.937 4976 Z= 0.389 Chirality : 0.045 0.135 556 Planarity : 0.003 0.022 624 Dihedral : 6.619 26.879 512 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer: Outliers : 1.74 % Allowed : 19.19 % Favored : 79.07 % 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: -0.97 (0.35), residues: 468 helix: -4.60 (0.30), residues: 24 sheet: 0.19 (0.26), residues: 296 loop : -1.54 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 108 HIS 0.001 0.000 HIS C 87 PHE 0.008 0.002 PHE D 29 TYR 0.012 0.002 TYR D 22 ARG 0.003 0.000 ARG A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.74 seconds wall clock time: 33 minutes 18.17 seconds (1998.17 seconds total)