Starting phenix.real_space_refine on Tue Feb 13 06:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrm_34978/02_2024/8hrm_34978.pdb" } resolution = 2.56 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= 0.009 sd= 0.064 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 "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.29, 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: 1.38 Conformation dependent library (CDL) restraints added in 778.4 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 4.2% alpha, 49.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.589A pdb=" N SER A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.553A pdb=" N SER B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.585A pdb=" N SER C 122 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.601A pdb=" N SER D 122 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.401A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.710A 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: 5.385A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.644A 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: 5.432A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.632A 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: 5.385A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 480 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: 0.99 Time building geometry restraints manager: 1.51 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 - 1.35: 584 1.35 - 1.42: 480 1.42 - 1.48: 620 1.48 - 1.55: 1380 Bond restraints: 3636 Sorted by residual: bond pdb=" CB THR D 91 " pdb=" CG2 THR D 91 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CG LEU B 109 " pdb=" CD1 LEU B 109 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" CG LEU A 109 " pdb=" CD1 LEU A 109 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.53e+00 bond pdb=" CB THR B 91 " pdb=" CG2 THR B 91 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.42e+00 bond pdb=" CG LEU C 109 " pdb=" CD1 LEU C 109 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 103.23 - 109.38: 446 109.38 - 115.54: 1865 115.54 - 121.70: 1641 121.70 - 127.85: 964 127.85 - 134.01: 60 Bond angle restraints: 4976 Sorted by residual: angle pdb=" N GLU B 44 " pdb=" CA GLU B 44 " pdb=" C GLU B 44 " ideal model delta sigma weight residual 108.07 113.07 -5.00 1.38e+00 5.25e-01 1.31e+01 angle pdb=" N GLU A 44 " pdb=" CA GLU A 44 " pdb=" C GLU A 44 " ideal model delta sigma weight residual 108.07 112.96 -4.89 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N GLU C 44 " pdb=" CA GLU C 44 " pdb=" C GLU C 44 " ideal model delta sigma weight residual 108.07 112.87 -4.80 1.38e+00 5.25e-01 1.21e+01 angle pdb=" N GLU D 44 " pdb=" CA GLU D 44 " pdb=" C GLU D 44 " ideal model delta sigma weight residual 108.07 112.77 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" C GLU C 44 " pdb=" CA GLU C 44 " pdb=" CB GLU C 44 " ideal model delta sigma weight residual 114.41 106.87 7.54 2.30e+00 1.89e-01 1.08e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.61: 1689 14.61 - 29.23: 208 29.23 - 43.84: 58 43.84 - 58.45: 25 58.45 - 73.06: 4 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA TRP D 79 " pdb=" C TRP D 79 " pdb=" N LYS D 80 " pdb=" CA LYS D 80 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TRP B 79 " pdb=" C TRP B 79 " pdb=" N LYS B 80 " pdb=" CA LYS B 80 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU C 44 " pdb=" C GLU C 44 " pdb=" N SER C 45 " pdb=" CA SER C 45 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 297 0.032 - 0.064: 193 0.064 - 0.096: 32 0.096 - 0.129: 20 0.129 - 0.161: 14 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TRP D 79 " pdb=" N TRP D 79 " pdb=" C TRP D 79 " pdb=" CB TRP D 79 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA TRP B 79 " pdb=" N TRP B 79 " pdb=" C TRP B 79 " pdb=" CB TRP B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 79 " 0.021 2.00e-02 2.50e+03 1.35e-02 4.53e+00 pdb=" CG TRP D 79 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 79 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 79 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 79 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 79 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 79 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 79 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 79 " 0.020 2.00e-02 2.50e+03 1.23e-02 3.76e+00 pdb=" CG TRP B 79 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 79 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 79 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 79 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 79 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 79 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 79 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 79 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 79 " -0.019 2.00e-02 2.50e+03 1.17e-02 3.44e+00 pdb=" CG TRP A 79 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 79 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 79 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 79 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 79 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 79 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 79 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 79 " -0.001 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 161 2.69 - 3.24: 3401 3.24 - 3.80: 6327 3.80 - 4.35: 8100 4.35 - 4.90: 13882 Nonbonded interactions: 31871 Sorted by model distance: nonbonded pdb=" O THR D 57 " pdb=" O HOH D 201 " model vdw 2.138 2.440 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR D 111 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR B 111 " pdb=" OG SER D 93 " model vdw 2.155 2.440 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR C 111 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR A 111 " pdb=" OG SER C 93 " model vdw 2.201 2.440 ... (remaining 31866 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: 0.010 Extract box with map and model: 1.820 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3636 Z= 0.332 Angle : 0.817 9.066 4976 Z= 0.424 Chirality : 0.047 0.161 556 Planarity : 0.004 0.053 624 Dihedral : 15.716 73.064 1160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 4.07 % Allowed : 28.78 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.38), residues: 468 helix: -3.02 (0.74), residues: 24 sheet: -1.36 (0.28), residues: 284 loop : -0.11 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 79 HIS 0.004 0.002 HIS A 87 PHE 0.011 0.002 PHE C 29 TYR 0.022 0.002 TYR B 54 ARG 0.010 0.001 ARG B 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 82 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.371 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.5942 time to fit residues: 51.0042 Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3636 Z= 0.191 Angle : 0.646 5.611 4976 Z= 0.341 Chirality : 0.043 0.137 556 Planarity : 0.003 0.031 624 Dihedral : 5.920 23.449 521 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.77 % Favored : 93.38 % Rotamer: Outliers : 6.40 % Allowed : 26.16 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.38), residues: 468 helix: -2.72 (0.76), residues: 24 sheet: -1.21 (0.27), residues: 288 loop : 0.05 (0.56), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.002 0.001 HIS A 87 PHE 0.008 0.001 PHE C 29 TYR 0.010 0.001 TYR C 54 ARG 0.007 0.001 ARG D 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 89 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.350 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 82 average time/residue: 0.6224 time to fit residues: 53.9502 Evaluate side-chains 71 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3636 Z= 0.354 Angle : 0.724 6.470 4976 Z= 0.376 Chirality : 0.047 0.151 556 Planarity : 0.003 0.034 624 Dihedral : 6.264 25.660 519 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.64 % Allowed : 4.91 % Favored : 94.44 % Rotamer: Outliers : 7.56 % Allowed : 27.91 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.38), residues: 468 helix: -2.42 (0.87), residues: 24 sheet: -1.06 (0.27), residues: 280 loop : -0.26 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 75 HIS 0.005 0.002 HIS A 87 PHE 0.013 0.002 PHE B 29 TYR 0.015 0.001 TYR B 54 ARG 0.007 0.001 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 92 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.382 Fit side-chains REVERT: B 79 TRP cc_start: 0.7059 (m100) cc_final: 0.6553 (m-90) outliers start: 26 outliers final: 13 residues processed: 86 average time/residue: 0.7095 time to fit residues: 64.0643 Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3636 Z= 0.223 Angle : 0.661 6.178 4976 Z= 0.339 Chirality : 0.045 0.145 556 Planarity : 0.003 0.032 624 Dihedral : 5.911 26.790 519 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.56 % Allowed : 29.94 % Favored : 62.50 % 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: -1.37 (0.38), residues: 468 helix: -2.09 (0.90), residues: 24 sheet: -0.91 (0.28), residues: 280 loop : -0.31 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.002 0.001 HIS A 87 PHE 0.010 0.002 PHE A 29 TYR 0.011 0.001 TYR C 54 ARG 0.007 0.001 ARG B 84 *********************** 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 91 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 65 time to evaluate : 0.327 Fit side-chains REVERT: A 25 LEU cc_start: 0.8339 (mm) cc_final: 0.8137 (mp) REVERT: B 25 LEU cc_start: 0.8353 (mm) cc_final: 0.8144 (mp) REVERT: B 79 TRP cc_start: 0.7031 (m100) cc_final: 0.6292 (m-90) outliers start: 26 outliers final: 16 residues processed: 81 average time/residue: 0.7912 time to fit residues: 66.8648 Evaluate side-chains 79 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 129 THR 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: 10.0000 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3636 Z= 0.338 Angle : 0.750 8.949 4976 Z= 0.381 Chirality : 0.047 0.157 556 Planarity : 0.003 0.045 624 Dihedral : 6.232 27.771 519 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.40 % Allowed : 32.85 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.37), residues: 468 helix: -2.29 (0.82), residues: 24 sheet: -1.03 (0.27), residues: 280 loop : -0.38 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.004 0.002 HIS A 87 PHE 0.013 0.002 PHE B 29 TYR 0.011 0.001 TYR B 54 ARG 0.010 0.001 ARG B 84 *********************** 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 87 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.377 Fit side-chains REVERT: A 25 LEU cc_start: 0.8313 (mm) cc_final: 0.8111 (mp) REVERT: A 79 TRP cc_start: 0.7068 (m100) cc_final: 0.6520 (m-90) REVERT: B 79 TRP cc_start: 0.7055 (m100) cc_final: 0.6373 (m-90) REVERT: D 79 TRP cc_start: 0.7045 (m100) cc_final: 0.6571 (m-90) outliers start: 22 outliers final: 12 residues processed: 79 average time/residue: 0.7805 time to fit residues: 64.4620 Evaluate side-chains 75 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 3636 Z= 0.553 Angle : 0.862 8.089 4976 Z= 0.445 Chirality : 0.053 0.176 556 Planarity : 0.004 0.027 624 Dihedral : 7.160 33.976 519 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 7.27 % Allowed : 31.40 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.35), residues: 468 helix: -2.89 (0.68), residues: 24 sheet: -1.36 (0.26), residues: 280 loop : -0.48 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 75 HIS 0.004 0.002 HIS A 87 PHE 0.016 0.003 PHE A 29 TYR 0.013 0.002 TYR B 54 ARG 0.007 0.001 ARG D 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 97 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 0.373 Fit side-chains REVERT: A 79 TRP cc_start: 0.7119 (m100) cc_final: 0.6618 (m-90) REVERT: B 79 TRP cc_start: 0.7087 (m100) cc_final: 0.6508 (m-90) REVERT: B 107 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: D 79 TRP cc_start: 0.7073 (m100) cc_final: 0.6527 (m-90) outliers start: 25 outliers final: 13 residues processed: 92 average time/residue: 0.7667 time to fit residues: 73.7637 Evaluate side-chains 85 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 THR 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: 4.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3636 Z= 0.301 Angle : 0.753 6.879 4976 Z= 0.384 Chirality : 0.049 0.162 556 Planarity : 0.004 0.048 624 Dihedral : 6.556 28.219 519 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.94 % Allowed : 34.30 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.36), residues: 468 helix: -2.78 (0.68), residues: 24 sheet: -1.28 (0.27), residues: 280 loop : -0.51 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 92 HIS 0.003 0.001 HIS A 87 PHE 0.012 0.002 PHE B 29 TYR 0.010 0.001 TYR C 54 ARG 0.014 0.001 ARG D 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 91 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.379 Fit side-chains REVERT: A 79 TRP cc_start: 0.7142 (m100) cc_final: 0.6628 (m-90) REVERT: B 79 TRP cc_start: 0.7117 (m100) cc_final: 0.6432 (m-90) REVERT: D 79 TRP cc_start: 0.7123 (m100) cc_final: 0.6596 (m-90) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.7676 time to fit residues: 68.1804 Evaluate side-chains 86 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3636 Z= 0.245 Angle : 0.722 6.352 4976 Z= 0.375 Chirality : 0.046 0.146 556 Planarity : 0.003 0.047 624 Dihedral : 6.263 28.853 519 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.23 % Allowed : 34.88 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.36), residues: 468 helix: -2.26 (0.79), residues: 24 sheet: -1.22 (0.27), residues: 280 loop : -0.50 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 92 HIS 0.002 0.001 HIS A 87 PHE 0.011 0.002 PHE B 29 TYR 0.010 0.001 TYR C 54 ARG 0.011 0.001 ARG B 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 94 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.425 Fit side-chains REVERT: A 79 TRP cc_start: 0.7116 (m100) cc_final: 0.6636 (m-90) REVERT: A 101 GLU cc_start: 0.6840 (pp20) cc_final: 0.6338 (pp20) REVERT: B 79 TRP cc_start: 0.7074 (m100) cc_final: 0.6308 (m-90) REVERT: D 79 TRP cc_start: 0.7146 (m100) cc_final: 0.6572 (m-90) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.8289 time to fit residues: 73.4851 Evaluate side-chains 86 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3636 Z= 0.196 Angle : 0.723 6.678 4976 Z= 0.373 Chirality : 0.045 0.148 556 Planarity : 0.004 0.058 624 Dihedral : 6.051 33.590 519 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.07 % Allowed : 37.21 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.73 (0.36), residues: 468 helix: -1.60 (0.95), residues: 24 sheet: -1.18 (0.27), residues: 280 loop : -0.58 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.001 0.000 HIS A 87 PHE 0.009 0.002 PHE D 29 TYR 0.013 0.001 TYR C 54 ARG 0.014 0.001 ARG D 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 88 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.391 Fit side-chains REVERT: A 79 TRP cc_start: 0.7125 (m100) cc_final: 0.6688 (m-90) REVERT: B 79 TRP cc_start: 0.7065 (m100) cc_final: 0.6745 (m-90) REVERT: C 84 ARG cc_start: 0.7018 (mtp180) cc_final: 0.6756 (mtp180) REVERT: D 79 TRP cc_start: 0.7069 (m100) cc_final: 0.6509 (m-90) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.7456 time to fit residues: 63.9828 Evaluate side-chains 76 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 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: 8.9990 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3636 Z= 0.411 Angle : 0.873 7.494 4976 Z= 0.453 Chirality : 0.051 0.158 556 Planarity : 0.006 0.087 624 Dihedral : 6.771 45.032 518 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.65 % Allowed : 36.92 % Favored : 58.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.92 (0.35), residues: 468 helix: -1.94 (0.86), residues: 24 sheet: -1.27 (0.27), residues: 280 loop : -0.76 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 75 HIS 0.003 0.002 HIS A 87 PHE 0.012 0.002 PHE B 29 TYR 0.014 0.002 TYR C 54 ARG 0.021 0.002 ARG B 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 86 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.396 Fit side-chains REVERT: A 79 TRP cc_start: 0.7149 (m100) cc_final: 0.6527 (m-90) REVERT: B 79 TRP cc_start: 0.7059 (m100) cc_final: 0.6360 (m-90) REVERT: D 79 TRP cc_start: 0.7108 (m100) cc_final: 0.6573 (m-90) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.7485 time to fit residues: 63.5245 Evaluate side-chains 81 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167476 restraints weight = 4398.567| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.45 r_work: 0.4044 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3636 Z= 0.269 Angle : 0.780 7.411 4976 Z= 0.404 Chirality : 0.047 0.152 556 Planarity : 0.005 0.088 624 Dihedral : 6.098 32.829 517 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.65 % Allowed : 36.92 % Favored : 58.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.00 (0.35), residues: 468 helix: -1.97 (0.84), residues: 24 sheet: -1.31 (0.27), residues: 280 loop : -0.83 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 75 HIS 0.002 0.001 HIS A 87 PHE 0.009 0.002 PHE D 29 TYR 0.013 0.001 TYR C 54 ARG 0.020 0.001 ARG B 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.65 seconds wall clock time: 30 minutes 4.28 seconds (1804.28 seconds total)