Starting phenix.real_space_refine on Tue Mar 3 11:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_34978.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_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/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_34978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_34978.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_34978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrm_34978/03_2026/8hrm_34978.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.93, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 142.1 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: 0.13 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: 0.56 Time building geometry restraints manager: 0.37 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: 0.00 - 1.81: 4820 1.81 - 3.63: 113 3.63 - 5.44: 25 5.44 - 7.25: 12 7.25 - 9.07: 6 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 3.040 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR D 111 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 111 " pdb=" OG SER D 93 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR C 111 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR A 111 " pdb=" OG SER C 93 " model vdw 2.201 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- 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= 0.234 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG B 84 TYR 0.022 0.002 TYR B 54 PHE 0.011 0.002 PHE C 29 TRP 0.036 0.003 TRP D 79 HIS 0.004 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 3636) covalent geometry : angle 0.81667 ( 4976) hydrogen bonds : bond 0.24011 ( 184) hydrogen bonds : angle 11.60207 ( 480) *********************** 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 to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.123 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.3114 time to fit residues: 26.5397 Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 49 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.195792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.170417 restraints weight = 4525.210| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.48 r_work: 0.4081 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3636 Z= 0.155 Angle : 0.685 5.864 4976 Z= 0.361 Chirality : 0.045 0.146 556 Planarity : 0.004 0.032 624 Dihedral : 6.107 24.043 521 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 8.14 % Allowed : 22.67 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.38), residues: 468 helix: -2.84 (0.76), residues: 24 sheet: -1.17 (0.27), residues: 284 loop : -0.13 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 84 TYR 0.009 0.001 TYR C 54 PHE 0.009 0.002 PHE C 29 TRP 0.016 0.002 TRP D 79 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3636) covalent geometry : angle 0.68545 ( 4976) hydrogen bonds : bond 0.03933 ( 184) hydrogen bonds : angle 8.19410 ( 480) *********************** 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 95 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.124 Fit side-chains REVERT: B 44 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: C 95 GLN cc_start: 0.8124 (pt0) cc_final: 0.7921 (pt0) REVERT: D 95 GLN cc_start: 0.8140 (pt0) cc_final: 0.7925 (pt0) outliers start: 28 outliers final: 16 residues processed: 87 average time/residue: 0.2937 time to fit residues: 26.9289 Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 52 SER 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 44 GLU Chi-restraints excluded: chain B residue 52 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 52 SER Chi-restraints excluded: chain D residue 112 SER 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 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.192609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165103 restraints weight = 4471.952| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.55 r_work: 0.4007 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 3636 Z= 0.249 Angle : 0.764 6.289 4976 Z= 0.396 Chirality : 0.048 0.154 556 Planarity : 0.004 0.048 624 Dihedral : 6.453 26.391 519 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.34 % Favored : 94.02 % Rotamer: Outliers : 6.40 % Allowed : 29.65 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.38), residues: 468 helix: -2.80 (0.79), residues: 24 sheet: -1.12 (0.28), residues: 284 loop : -0.11 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 84 TYR 0.012 0.002 TYR B 54 PHE 0.012 0.002 PHE B 29 TRP 0.012 0.002 TRP D 75 HIS 0.004 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 3636) covalent geometry : angle 0.76415 ( 4976) hydrogen bonds : bond 0.03771 ( 184) hydrogen bonds : angle 7.88809 ( 480) *********************** 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 81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.160 Fit side-chains REVERT: B 79 TRP cc_start: 0.7106 (m100) cc_final: 0.6670 (m-90) outliers start: 22 outliers final: 13 residues processed: 76 average time/residue: 0.3732 time to fit residues: 29.6385 Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 44 GLU 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 112 SER 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 3 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.194313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.168136 restraints weight = 4459.160| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.51 r_work: 0.4045 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2043 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= 0.166 Angle : 0.696 5.977 4976 Z= 0.358 Chirality : 0.045 0.148 556 Planarity : 0.004 0.055 624 Dihedral : 6.114 27.447 519 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.56 % Allowed : 28.78 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.37), residues: 468 helix: -2.73 (0.78), residues: 24 sheet: -0.94 (0.28), residues: 280 loop : -0.46 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 84 TYR 0.010 0.001 TYR C 54 PHE 0.010 0.002 PHE C 29 TRP 0.010 0.001 TRP A 92 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3636) covalent geometry : angle 0.69572 ( 4976) hydrogen bonds : bond 0.03260 ( 184) hydrogen bonds : angle 7.49012 ( 480) *********************** 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 87 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.138 Fit side-chains REVERT: B 79 TRP cc_start: 0.7114 (m100) cc_final: 0.6348 (m-90) REVERT: D 79 TRP cc_start: 0.7045 (m100) cc_final: 0.6340 (m-90) outliers start: 26 outliers final: 15 residues processed: 80 average time/residue: 0.3391 time to fit residues: 28.3931 Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 52 SER 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 44 GLU 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 112 SER 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 13 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 87 HIS ** 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 = 0.4369 r_free = 0.4369 target = 0.190512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163216 restraints weight = 4534.676| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.52 r_work: 0.3989 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 3636 Z= 0.289 Angle : 0.805 6.536 4976 Z= 0.418 Chirality : 0.049 0.157 556 Planarity : 0.004 0.033 624 Dihedral : 6.700 29.482 519 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.56 % Allowed : 30.23 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.37), residues: 468 helix: -3.10 (0.68), residues: 24 sheet: -1.11 (0.28), residues: 280 loop : -0.46 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 84 TYR 0.012 0.002 TYR C 54 PHE 0.014 0.002 PHE A 29 TRP 0.014 0.002 TRP D 75 HIS 0.004 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 3636) covalent geometry : angle 0.80470 ( 4976) hydrogen bonds : bond 0.03682 ( 184) hydrogen bonds : angle 7.70234 ( 480) *********************** 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 90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.092 Fit side-chains REVERT: A 79 TRP cc_start: 0.7042 (m100) cc_final: 0.6384 (m-90) REVERT: D 79 TRP cc_start: 0.6967 (m100) cc_final: 0.6464 (m-90) outliers start: 26 outliers final: 16 residues processed: 83 average time/residue: 0.3538 time to fit residues: 30.6464 Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 52 SER 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 44 GLU 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 52 SER 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 112 SER 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 18 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 87 HIS ** 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 = 0.4393 r_free = 0.4393 target = 0.192852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166387 restraints weight = 4529.272| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.56 r_work: 0.4029 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3636 Z= 0.190 Angle : 0.719 6.379 4976 Z= 0.373 Chirality : 0.046 0.152 556 Planarity : 0.003 0.036 624 Dihedral : 6.349 27.679 519 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.69 % Allowed : 31.40 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.36), residues: 468 helix: -2.91 (0.72), residues: 24 sheet: -1.15 (0.28), residues: 280 loop : -0.45 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 84 TYR 0.011 0.001 TYR C 54 PHE 0.011 0.002 PHE C 29 TRP 0.012 0.001 TRP A 92 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3636) covalent geometry : angle 0.71928 ( 4976) hydrogen bonds : bond 0.03257 ( 184) hydrogen bonds : angle 7.39800 ( 480) *********************** 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 87 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.133 Fit side-chains REVERT: A 79 TRP cc_start: 0.7119 (m100) cc_final: 0.6497 (m-90) REVERT: B 79 TRP cc_start: 0.7056 (m100) cc_final: 0.6229 (m-90) REVERT: D 79 TRP cc_start: 0.7024 (m100) cc_final: 0.6402 (m-90) outliers start: 23 outliers final: 16 residues processed: 79 average time/residue: 0.3865 time to fit residues: 31.8140 Evaluate side-chains 78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 52 SER 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 44 GLU 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 52 SER 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 112 SER 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 21 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 87 HIS ** 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 = 0.4368 r_free = 0.4368 target = 0.190814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.163244 restraints weight = 4583.594| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.51 r_work: 0.3984 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 3636 Z= 0.287 Angle : 0.833 7.005 4976 Z= 0.432 Chirality : 0.052 0.169 556 Planarity : 0.004 0.042 624 Dihedral : 6.832 30.461 519 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 7.56 % Allowed : 31.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.36), residues: 468 helix: -3.12 (0.67), residues: 24 sheet: -1.30 (0.27), residues: 280 loop : -0.52 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 84 TYR 0.013 0.002 TYR C 54 PHE 0.015 0.002 PHE A 29 TRP 0.013 0.002 TRP D 75 HIS 0.003 0.002 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 3636) covalent geometry : angle 0.83337 ( 4976) hydrogen bonds : bond 0.03636 ( 184) hydrogen bonds : angle 7.60437 ( 480) *********************** 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 90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.132 Fit side-chains REVERT: A 79 TRP cc_start: 0.7083 (m100) cc_final: 0.6525 (m-90) REVERT: B 79 TRP cc_start: 0.7041 (m100) cc_final: 0.6299 (m-90) REVERT: B 84 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7031 (ptm160) REVERT: B 101 GLU cc_start: 0.6659 (pp20) cc_final: 0.6250 (pp20) REVERT: D 79 TRP cc_start: 0.6982 (m100) cc_final: 0.6470 (m-90) REVERT: D 84 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6926 (ptm160) REVERT: D 101 GLU cc_start: 0.6665 (pp20) cc_final: 0.6251 (pp20) outliers start: 26 outliers final: 17 residues processed: 83 average time/residue: 0.3636 time to fit residues: 31.4484 Evaluate side-chains 80 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 52 SER 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 44 GLU 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 52 SER 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 52 SER Chi-restraints excluded: chain D residue 112 SER 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 18 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 85 ASN D 87 HIS ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.194547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.168440 restraints weight = 4552.538| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.53 r_work: 0.4052 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2619 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= 0.152 Angle : 0.742 7.013 4976 Z= 0.379 Chirality : 0.048 0.155 556 Planarity : 0.003 0.034 624 Dihedral : 6.247 30.026 519 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.52 % Allowed : 33.43 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.35), residues: 468 helix: -2.76 (0.75), residues: 24 sheet: -1.25 (0.27), residues: 280 loop : -0.61 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 84 TYR 0.011 0.001 TYR C 54 PHE 0.010 0.002 PHE B 29 TRP 0.011 0.001 TRP A 92 HIS 0.001 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3636) covalent geometry : angle 0.74178 ( 4976) hydrogen bonds : bond 0.03096 ( 184) hydrogen bonds : angle 7.20941 ( 480) *********************** 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 90 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.133 Fit side-chains REVERT: A 79 TRP cc_start: 0.7107 (m100) cc_final: 0.6253 (m-90) REVERT: B 44 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: B 79 TRP cc_start: 0.7083 (m100) cc_final: 0.6235 (m-90) REVERT: B 84 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6954 (ptm160) REVERT: D 79 TRP cc_start: 0.7039 (m100) cc_final: 0.6399 (m-90) REVERT: D 84 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6977 (ptm160) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.4004 time to fit residues: 34.1296 Evaluate side-chains 83 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 44 GLU 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 52 SER 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 112 SER 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 4 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.191304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165167 restraints weight = 4471.658| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.51 r_work: 0.4021 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3636 Z= 0.231 Angle : 0.829 7.800 4976 Z= 0.427 Chirality : 0.050 0.163 556 Planarity : 0.004 0.047 624 Dihedral : 6.518 34.766 519 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.07 % Allowed : 35.17 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.36), residues: 468 helix: -2.76 (0.76), residues: 24 sheet: -1.26 (0.27), residues: 280 loop : -0.62 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 84 TYR 0.013 0.001 TYR C 54 PHE 0.012 0.002 PHE B 29 TRP 0.013 0.002 TRP D 75 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 3636) covalent geometry : angle 0.82883 ( 4976) hydrogen bonds : bond 0.03393 ( 184) hydrogen bonds : angle 7.33342 ( 480) *********************** 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 84 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.133 Fit side-chains REVERT: A 79 TRP cc_start: 0.7125 (m100) cc_final: 0.6365 (m-90) REVERT: B 79 TRP cc_start: 0.7044 (m100) cc_final: 0.6279 (m-90) REVERT: B 84 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6916 (ptm160) REVERT: D 79 TRP cc_start: 0.7011 (m100) cc_final: 0.6381 (m-90) REVERT: D 84 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6899 (ptm160) outliers start: 14 outliers final: 14 residues processed: 80 average time/residue: 0.4083 time to fit residues: 33.9151 Evaluate side-chains 82 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU 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 44 GLU 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 112 SER 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 40 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.193127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166998 restraints weight = 4548.286| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.53 r_work: 0.4041 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3636 Z= 0.180 Angle : 0.783 8.005 4976 Z= 0.402 Chirality : 0.048 0.163 556 Planarity : 0.003 0.029 624 Dihedral : 6.226 30.480 519 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.07 % Allowed : 36.05 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.35), residues: 468 helix: -2.67 (0.77), residues: 24 sheet: -1.32 (0.27), residues: 280 loop : -0.70 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 84 TYR 0.014 0.001 TYR C 54 PHE 0.011 0.002 PHE C 29 TRP 0.012 0.001 TRP C 79 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3636) covalent geometry : angle 0.78266 ( 4976) hydrogen bonds : bond 0.03222 ( 184) hydrogen bonds : angle 7.20134 ( 480) ********************** 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 81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.084 Fit side-chains REVERT: A 79 TRP cc_start: 0.7101 (m100) cc_final: 0.6324 (m-90) REVERT: B 84 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6969 (ptm160) REVERT: B 101 GLU cc_start: 0.6677 (pp20) cc_final: 0.6186 (pp20) REVERT: D 79 TRP cc_start: 0.7028 (m100) cc_final: 0.6349 (m-90) REVERT: D 101 GLU cc_start: 0.6695 (pp20) cc_final: 0.6178 (pp20) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.4039 time to fit residues: 32.2928 Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 44 GLU 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 112 SER 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 27 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4388 r_free = 0.4388 target = 0.192072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166144 restraints weight = 4437.306| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.49 r_work: 0.4038 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3636 Z= 0.204 Angle : 0.821 8.063 4976 Z= 0.422 Chirality : 0.049 0.164 556 Planarity : 0.004 0.060 624 Dihedral : 6.314 31.889 518 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.36 % Allowed : 36.05 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.35), residues: 468 helix: -2.64 (0.77), residues: 24 sheet: -1.32 (0.27), residues: 280 loop : -0.68 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 84 TYR 0.013 0.001 TYR C 54 PHE 0.011 0.002 PHE B 29 TRP 0.012 0.002 TRP D 75 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 3636) covalent geometry : angle 0.82093 ( 4976) hydrogen bonds : bond 0.03305 ( 184) hydrogen bonds : angle 7.22749 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.50 seconds wall clock time: 22 minutes 11.00 seconds (1331.00 seconds total)