Starting phenix.real_space_refine on Sat Apr 4 21:31:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9m_63734/04_2026/9m9m_63734.map" } resolution = 2.52 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= 0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 26 5.16 5 C 2629 2.51 5 N 646 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3995 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1946 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2003 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' K': 1, 'ACD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' K': 1, 'ACD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.11, per 1000 atoms: 0.28 Number of scatterers: 3995 At special positions: 0 Unit cell: (71.912, 66.256, 86.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 26 16.00 O 692 8.00 N 646 7.00 C 2629 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: 0.33 Conformation dependent library (CDL) restraints added in 180.5 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 14 through 43 Processing helix chain 'A' and resid 44 through 62 removed outlier: 3.643A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 removed outlier: 3.770A pdb=" N LEU A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 122 through 160 removed outlier: 4.280A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 293 Processing helix chain 'B' and resid 15 through 42 Processing helix chain 'B' and resid 42 through 64 removed outlier: 4.068A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.798A pdb=" N LEU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 122 through 164 removed outlier: 3.531A pdb=" N PHE B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 220 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 293 removed outlier: 3.551A pdb=" N LYS B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 1002 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: 0.59 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1231 1.34 - 1.46: 845 1.46 - 1.57: 1971 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4083 Sorted by residual: bond pdb=" C16 ACD B 502 " pdb=" C17 ACD B 502 " ideal model delta sigma weight residual 1.530 1.490 0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C16 ACD A 501 " pdb=" C17 ACD A 501 " ideal model delta sigma weight residual 1.530 1.490 0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" CG1 ILE A 200 " pdb=" CD1 ILE A 200 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.26e+00 bond pdb=" C8 ACD A 501 " pdb=" C9 ACD A 501 " ideal model delta sigma weight residual 1.332 1.303 0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CB LYS A 293 " pdb=" CG LYS A 293 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 ... (remaining 4078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 5484 3.78 - 7.57: 26 7.57 - 11.35: 2 11.35 - 15.14: 0 15.14 - 18.92: 3 Bond angle restraints: 5515 Sorted by residual: angle pdb=" CA LEU B 31 " pdb=" CB LEU B 31 " pdb=" CG LEU B 31 " ideal model delta sigma weight residual 116.30 135.22 -18.92 3.50e+00 8.16e-02 2.92e+01 angle pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " pdb=" CG LEU A 31 " ideal model delta sigma weight residual 116.30 132.74 -16.44 3.50e+00 8.16e-02 2.21e+01 angle pdb=" CA LEU B 21 " pdb=" CB LEU B 21 " pdb=" CG LEU B 21 " ideal model delta sigma weight residual 116.30 131.80 -15.50 3.50e+00 8.16e-02 1.96e+01 angle pdb=" CB LYS A 293 " pdb=" CG LYS A 293 " pdb=" CD LYS A 293 " ideal model delta sigma weight residual 111.30 119.70 -8.40 2.30e+00 1.89e-01 1.33e+01 angle pdb=" CA GLN A 48 " pdb=" CB GLN A 48 " pdb=" CG GLN A 48 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 5510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 1996 16.35 - 32.70: 238 32.70 - 49.06: 85 49.06 - 65.41: 28 65.41 - 81.76: 7 Dihedral angle restraints: 2354 sinusoidal: 892 harmonic: 1462 Sorted by residual: dihedral pdb=" CA SER A 253 " pdb=" C SER A 253 " pdb=" N GLN A 254 " pdb=" CA GLN A 254 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 148 " pdb=" CD ARG A 148 " pdb=" NE ARG A 148 " pdb=" CZ ARG A 148 " ideal model delta sinusoidal sigma weight residual 90.00 46.78 43.22 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CA GLU A 46 " pdb=" CB GLU A 46 " pdb=" CG GLU A 46 " pdb=" CD GLU A 46 " ideal model delta sinusoidal sigma weight residual -180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 532 0.057 - 0.113: 81 0.113 - 0.170: 7 0.170 - 0.227: 1 0.227 - 0.284: 2 Chirality restraints: 623 Sorted by residual: chirality pdb=" CG LEU B 21 " pdb=" CB LEU B 21 " pdb=" CD1 LEU B 21 " pdb=" CD2 LEU B 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU A 31 " pdb=" CB LEU A 31 " pdb=" CD1 LEU A 31 " pdb=" CD2 LEU A 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU B 31 " pdb=" CB LEU B 31 " pdb=" CD1 LEU B 31 " pdb=" CD2 LEU B 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 620 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 ACD A 501 " 0.251 2.00e-02 2.50e+03 2.38e-01 5.68e+02 pdb=" C5 ACD A 501 " -0.373 2.00e-02 2.50e+03 pdb=" C6 ACD A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C7 ACD A 501 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 ACD B 502 " -0.089 2.00e-02 2.50e+03 1.80e-01 3.22e+02 pdb=" C7 ACD B 502 " 0.085 2.00e-02 2.50e+03 pdb=" C8 ACD B 502 " -0.236 2.00e-02 2.50e+03 pdb=" C9 ACD B 502 " 0.241 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 ACD B 502 " -0.060 2.00e-02 2.50e+03 1.15e-01 1.32e+02 pdb=" C14 ACD B 502 " 0.150 2.00e-02 2.50e+03 pdb=" C15 ACD B 502 " -0.151 2.00e-02 2.50e+03 pdb=" C16 ACD B 502 " 0.061 2.00e-02 2.50e+03 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 975 2.78 - 3.37: 4938 3.37 - 3.96: 7871 3.96 - 4.55: 11317 4.55 - 5.14: 15887 Nonbonded interactions: 40988 Sorted by model distance: nonbonded pdb=" N GLU B 252 " pdb=" OE1 GLU B 252 " model vdw 2.188 3.120 nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.236 3.040 nonbonded pdb=" O PRO A 118 " pdb=" NZ LYS A 124 " model vdw 2.249 3.120 nonbonded pdb=" N SER B 67 " pdb=" OE2 GLU B 70 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.253 3.040 ... (remaining 40983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 or (resid 66 and (name N or n \ ame CA or name C or name O or name CB )) or resid 67 through 293)) selection = (chain 'B' and (resid 14 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 42 or (resid 43 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 95 or (resid 96 and (name N or name CA or name C or name O or name CB )) or \ resid 97 through 160 or resid 191 through 251 or (resid 252 and (name N or name \ CA or name C or name O or name CB )) or resid 253 through 293)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 5.650 Find NCS groups from input model: 0.190 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4083 Z= 0.200 Angle : 0.827 18.923 5515 Z= 0.407 Chirality : 0.042 0.284 623 Planarity : 0.013 0.238 689 Dihedral : 17.641 81.760 1418 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.97 % Allowed : 31.07 % Favored : 67.96 % 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: 2.29 (0.38), residues: 496 helix: 2.17 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -0.79 (0.66), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 148 TYR 0.030 0.002 TYR A 30 PHE 0.030 0.002 PHE A 225 TRP 0.009 0.001 TRP A 95 HIS 0.001 0.000 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4083) covalent geometry : angle 0.82695 ( 5515) hydrogen bonds : bond 0.14325 ( 334) hydrogen bonds : angle 5.94771 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.132 Fit side-chains REVERT: A 46 GLU cc_start: 0.6238 (pm20) cc_final: 0.5759 (pm20) REVERT: A 115 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6879 (ppp) REVERT: A 116 THR cc_start: 0.8630 (p) cc_final: 0.8143 (p) REVERT: B 246 SER cc_start: 0.7499 (t) cc_final: 0.7278 (p) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.4502 time to fit residues: 34.6496 Evaluate side-chains 67 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 288 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.179191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.169309 restraints weight = 5839.194| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.68 r_work: 0.4242 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4083 Z= 0.188 Angle : 0.655 10.549 5515 Z= 0.334 Chirality : 0.039 0.160 623 Planarity : 0.004 0.025 689 Dihedral : 9.142 59.082 590 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.07 % Allowed : 25.49 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.25 (0.38), residues: 496 helix: 2.05 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -0.60 (0.67), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 148 TYR 0.012 0.001 TYR B 130 PHE 0.026 0.002 PHE A 225 TRP 0.007 0.001 TRP A 222 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4083) covalent geometry : angle 0.65504 ( 5515) hydrogen bonds : bond 0.05485 ( 334) hydrogen bonds : angle 4.72069 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.140 Fit side-chains REVERT: A 115 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7334 (pmt) REVERT: A 293 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5677 (mmtm) REVERT: B 200 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7107 (mp) REVERT: B 246 SER cc_start: 0.8004 (t) cc_final: 0.7631 (p) outliers start: 25 outliers final: 7 residues processed: 89 average time/residue: 0.4683 time to fit residues: 43.2791 Evaluate side-chains 77 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 251 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN B 254 GLN B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.178246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.168136 restraints weight = 5801.634| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 1.71 r_work: 0.4239 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4083 Z= 0.189 Angle : 0.602 9.827 5515 Z= 0.317 Chirality : 0.039 0.161 623 Planarity : 0.004 0.061 689 Dihedral : 8.843 57.556 585 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.37 % Allowed : 27.18 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.04 (0.37), residues: 496 helix: 1.95 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.93 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.010 0.001 TYR B 130 PHE 0.016 0.002 PHE A 225 TRP 0.006 0.001 TRP A 95 HIS 0.001 0.000 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4083) covalent geometry : angle 0.60248 ( 5515) hydrogen bonds : bond 0.05318 ( 334) hydrogen bonds : angle 4.52753 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.093 Fit side-chains REVERT: B 200 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7027 (mp) outliers start: 18 outliers final: 7 residues processed: 78 average time/residue: 0.4025 time to fit residues: 32.7299 Evaluate side-chains 69 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.170440 restraints weight = 5686.943| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.72 r_work: 0.4262 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4083 Z= 0.175 Angle : 0.566 9.804 5515 Z= 0.301 Chirality : 0.038 0.175 623 Planarity : 0.004 0.053 689 Dihedral : 8.534 59.890 580 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.37 % Allowed : 27.67 % Favored : 67.96 % 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: 2.17 (0.37), residues: 496 helix: 2.06 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -0.92 (0.67), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.009 0.001 TYR B 196 PHE 0.015 0.002 PHE A 145 TRP 0.006 0.001 TRP A 95 HIS 0.001 0.000 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4083) covalent geometry : angle 0.56648 ( 5515) hydrogen bonds : bond 0.05085 ( 334) hydrogen bonds : angle 4.36930 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.135 Fit side-chains REVERT: A 20 PHE cc_start: 0.7174 (t80) cc_final: 0.6964 (t80) REVERT: A 201 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7828 (mt) REVERT: A 293 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5976 (mmtm) REVERT: B 91 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7807 (t) REVERT: B 115 MET cc_start: 0.7181 (mmp) cc_final: 0.6884 (mmp) REVERT: B 200 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 281 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7255 (mt) outliers start: 18 outliers final: 6 residues processed: 78 average time/residue: 0.4567 time to fit residues: 36.9955 Evaluate side-chains 73 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.179732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.169344 restraints weight = 5724.121| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 1.74 r_work: 0.4251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4116 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4083 Z= 0.189 Angle : 0.583 9.873 5515 Z= 0.309 Chirality : 0.040 0.197 623 Planarity : 0.004 0.030 689 Dihedral : 8.591 59.388 580 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.37 % Allowed : 28.64 % Favored : 66.99 % 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: 2.05 (0.37), residues: 496 helix: 1.96 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -1.01 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.009 0.001 TYR B 196 PHE 0.015 0.002 PHE B 60 TRP 0.006 0.001 TRP B 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4083) covalent geometry : angle 0.58305 ( 5515) hydrogen bonds : bond 0.05117 ( 334) hydrogen bonds : angle 4.37862 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.141 Fit side-chains REVERT: A 201 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 200 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7004 (mp) outliers start: 18 outliers final: 8 residues processed: 77 average time/residue: 0.4578 time to fit residues: 36.6740 Evaluate side-chains 73 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.180761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.170162 restraints weight = 5810.393| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.76 r_work: 0.4262 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4083 Z= 0.179 Angle : 0.593 9.706 5515 Z= 0.312 Chirality : 0.039 0.210 623 Planarity : 0.004 0.028 689 Dihedral : 8.559 59.909 580 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.58 % Allowed : 26.70 % Favored : 67.72 % 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: 2.12 (0.37), residues: 496 helix: 2.00 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -0.95 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.007 0.001 TYR B 196 PHE 0.045 0.002 PHE B 145 TRP 0.006 0.001 TRP B 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4083) covalent geometry : angle 0.59341 ( 5515) hydrogen bonds : bond 0.05018 ( 334) hydrogen bonds : angle 4.32267 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.150 Fit side-chains REVERT: A 197 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6193 (p) REVERT: A 201 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7832 (mt) REVERT: B 20 PHE cc_start: 0.7060 (t80) cc_final: 0.6782 (t80) REVERT: B 200 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6985 (mp) outliers start: 23 outliers final: 12 residues processed: 81 average time/residue: 0.4593 time to fit residues: 38.6255 Evaluate side-chains 77 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 39 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.183462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.173292 restraints weight = 5840.676| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.72 r_work: 0.4283 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4083 Z= 0.158 Angle : 0.570 9.340 5515 Z= 0.297 Chirality : 0.038 0.199 623 Planarity : 0.003 0.029 689 Dihedral : 8.464 59.411 580 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.10 % Allowed : 28.40 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.38 (0.37), residues: 496 helix: 2.18 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -0.74 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.007 0.001 TYR B 196 PHE 0.039 0.002 PHE B 145 TRP 0.005 0.001 TRP A 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4083) covalent geometry : angle 0.57010 ( 5515) hydrogen bonds : bond 0.04728 ( 334) hydrogen bonds : angle 4.22894 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.137 Fit side-chains REVERT: A 197 VAL cc_start: 0.6923 (OUTLIER) cc_final: 0.6135 (p) REVERT: B 200 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6916 (mp) outliers start: 21 outliers final: 13 residues processed: 82 average time/residue: 0.4561 time to fit residues: 38.9059 Evaluate side-chains 76 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.181567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.171559 restraints weight = 5746.800| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.70 r_work: 0.4266 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4083 Z= 0.187 Angle : 0.603 9.485 5515 Z= 0.316 Chirality : 0.040 0.248 623 Planarity : 0.003 0.026 689 Dihedral : 8.612 59.184 580 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.37 % Allowed : 29.37 % Favored : 66.26 % 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: 2.24 (0.37), residues: 496 helix: 2.07 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -0.75 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.009 0.001 TYR B 130 PHE 0.034 0.002 PHE B 145 TRP 0.005 0.001 TRP B 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4083) covalent geometry : angle 0.60308 ( 5515) hydrogen bonds : bond 0.05002 ( 334) hydrogen bonds : angle 4.31134 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.096 Fit side-chains REVERT: A 47 ARG cc_start: 0.7435 (tmm-80) cc_final: 0.7233 (tmm-80) REVERT: B 200 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6959 (mp) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.4473 time to fit residues: 37.2015 Evaluate side-chains 80 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.181596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.171343 restraints weight = 5830.865| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.75 r_work: 0.4264 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4083 Z= 0.193 Angle : 0.618 9.370 5515 Z= 0.322 Chirality : 0.040 0.236 623 Planarity : 0.004 0.052 689 Dihedral : 8.692 59.673 580 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.88 % Allowed : 30.34 % Favored : 65.78 % 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: 2.08 (0.37), residues: 496 helix: 1.96 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.83 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.010 0.001 TYR B 130 PHE 0.056 0.002 PHE A 145 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4083) covalent geometry : angle 0.61754 ( 5515) hydrogen bonds : bond 0.05050 ( 334) hydrogen bonds : angle 4.39669 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.136 Fit side-chains REVERT: B 20 PHE cc_start: 0.7065 (t80) cc_final: 0.6698 (t80) REVERT: B 200 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6958 (mp) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.4248 time to fit residues: 35.3668 Evaluate side-chains 74 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.181574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.171555 restraints weight = 5741.581| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.71 r_work: 0.4269 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4083 Z= 0.197 Angle : 0.641 9.576 5515 Z= 0.339 Chirality : 0.042 0.282 623 Planarity : 0.004 0.038 689 Dihedral : 8.711 59.838 580 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.88 % Allowed : 31.07 % Favored : 65.05 % 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: 1.92 (0.37), residues: 496 helix: 1.84 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -0.90 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.011 0.001 TYR B 130 PHE 0.037 0.002 PHE A 145 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4083) covalent geometry : angle 0.64134 ( 5515) hydrogen bonds : bond 0.05112 ( 334) hydrogen bonds : angle 4.43698 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.121 Fit side-chains REVERT: B 20 PHE cc_start: 0.7047 (t80) cc_final: 0.6655 (t80) REVERT: B 200 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6973 (mp) outliers start: 16 outliers final: 13 residues processed: 78 average time/residue: 0.4607 time to fit residues: 37.3609 Evaluate side-chains 80 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** B 59 ASN ** 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 = 0.4495 r_free = 0.4495 target = 0.185061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.175145 restraints weight = 5792.466| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.67 r_work: 0.4307 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4083 Z= 0.159 Angle : 0.617 9.401 5515 Z= 0.323 Chirality : 0.040 0.278 623 Planarity : 0.004 0.034 689 Dihedral : 8.561 59.763 580 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.64 % Allowed : 32.28 % Favored : 64.08 % 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: 2.27 (0.37), residues: 496 helix: 2.10 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -0.83 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.009 0.001 TYR B 130 PHE 0.061 0.002 PHE A 145 TRP 0.005 0.001 TRP A 95 HIS 0.001 0.000 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4083) covalent geometry : angle 0.61713 ( 5515) hydrogen bonds : bond 0.04643 ( 334) hydrogen bonds : angle 4.25027 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.57 seconds wall clock time: 28 minutes 44.76 seconds (1724.76 seconds total)