Starting phenix.real_space_refine on Wed Jul 1 23:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9m_63734/07_2026/9m9m_63734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9m_63734/07_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_63734/07_2026/9m9m_63734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9m_63734/07_2026/9m9m_63734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m9m_63734/07_2026/9m9m_63734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9m_63734/07_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-dev-6108/lib/python3.11/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, 22 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'ACD': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'ACD': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.97, per 1000 atoms: 0.24 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: 0.35 Conformation dependent library (CDL) restraints added in 150.7 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: 0.07 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: 0.58 Time building geometry restraints manager: 0.45 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.350 Find NCS groups from input model: 0.070 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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/Z covalent geometry : bond 0.00435 / 0.20 ( 4083) covalent geometry : angle 0.82695 / 0.41 ( 5515) hydrogen bonds : bond 0.14325 / 9.48 ( 334) hydrogen bonds : angle 5.94771 / 4.54 ( 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 : 0.154 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: 0.4179 time to fit residues: 32.1764 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 : 0.139 ------------------------------------------------------------------------------- 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: 0.0370 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.177506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.167641 restraints weight = 5884.307| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 1.69 r_work: 0.4226 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4083 Z= 0.202 Angle : 0.675 10.596 5515 Z= 0.344 Chirality : 0.040 0.167 623 Planarity : 0.004 0.025 689 Dihedral : 9.308 58.386 590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.31 % Allowed : 25.00 % Favored : 68.69 % 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: 1.99 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -1.05 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 148 TYR 0.015 0.001 TYR B 130 PHE 0.027 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/Z covalent geometry : bond 0.00416 / 0.20 ( 4083) covalent geometry : angle 0.67480 / 0.34 ( 5515) hydrogen bonds : bond 0.05594 / 3.72 ( 334) hydrogen bonds : angle 4.79274 / 3.64 ( 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 97 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7427 (pmt) REVERT: A 293 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5649 (mmtm) REVERT: B 200 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7095 (mp) REVERT: B 246 SER cc_start: 0.7992 (t) cc_final: 0.7620 (p) outliers start: 26 outliers final: 8 residues processed: 92 average time/residue: 0.4557 time to fit residues: 43.5910 Evaluate side-chains 79 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain B residue 149 LEU 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: 0.5980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.176646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.166904 restraints weight = 5765.576| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 1.67 r_work: 0.4231 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4083 Z= 0.191 Angle : 0.613 9.847 5515 Z= 0.323 Chirality : 0.039 0.162 623 Planarity : 0.005 0.067 689 Dihedral : 8.912 56.471 585 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 1.83 (0.37), residues: 496 helix: 1.92 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.011 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/Z covalent geometry : bond 0.00394 / 0.19 ( 4083) covalent geometry : angle 0.61288 / 0.32 ( 5515) hydrogen bonds : bond 0.05340 / 3.57 ( 334) hydrogen bonds : angle 4.59229 / 3.50 ( 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 85 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.085 Fit side-chains REVERT: B 200 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7048 (mp) REVERT: B 244 VAL cc_start: 0.7829 (p) cc_final: 0.7616 (t) REVERT: B 246 SER cc_start: 0.7973 (t) cc_final: 0.7572 (p) outliers start: 18 outliers final: 7 residues processed: 80 average time/residue: 0.2965 time to fit residues: 24.7777 Evaluate side-chains 70 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 0.0670 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.171413 restraints weight = 5737.499| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.71 r_work: 0.4276 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4083 Z= 0.146 Angle : 0.541 9.378 5515 Z= 0.289 Chirality : 0.038 0.175 623 Planarity : 0.004 0.041 689 Dihedral : 8.524 58.605 580 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.13 % Allowed : 27.43 % 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: 2.23 (0.37), residues: 496 helix: 2.25 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -1.54 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 87 TYR 0.009 0.001 TYR B 78 PHE 0.015 0.001 PHE A 145 TRP 0.006 0.001 TRP A 95 HIS 0.000 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 4083) covalent geometry : angle 0.54115 / 0.29 ( 5515) hydrogen bonds : bond 0.04712 / 3.15 ( 334) hydrogen bonds : angle 4.28181 / 3.28 ( 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: 17 poor density : 65 time to evaluate : 0.089 Fit side-chains REVERT: A 293 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5878 (mmtm) REVERT: B 244 VAL cc_start: 0.7860 (p) cc_final: 0.7624 (t) REVERT: B 246 SER cc_start: 0.7986 (t) cc_final: 0.7683 (t) REVERT: B 281 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7232 (mt) outliers start: 17 outliers final: 5 residues processed: 78 average time/residue: 0.4267 time to fit residues: 34.4845 Evaluate side-chains 71 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 199 LEU 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: 1.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.178500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.168414 restraints weight = 5710.396| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 1.68 r_work: 0.4243 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4083 Z= 0.195 Angle : 0.590 9.476 5515 Z= 0.313 Chirality : 0.039 0.177 623 Planarity : 0.004 0.054 689 Dihedral : 8.650 59.440 580 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 1.86 (0.37), residues: 496 helix: 1.96 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.64 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.009 0.001 TYR A 102 PHE 0.023 0.002 PHE B 145 TRP 0.008 0.001 TRP B 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 4083) covalent geometry : angle 0.59029 / 0.31 ( 5515) hydrogen bonds : bond 0.05221 / 3.49 ( 334) hydrogen bonds : angle 4.40607 / 3.36 ( 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 84 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.145 Fit side-chains REVERT: B 200 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7025 (mp) REVERT: B 244 VAL cc_start: 0.7883 (p) cc_final: 0.7639 (t) REVERT: B 246 SER cc_start: 0.8061 (t) cc_final: 0.7673 (p) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.3953 time to fit residues: 32.7177 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 : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 196 TYR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.179406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.169053 restraints weight = 5829.832| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.73 r_work: 0.4248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4113 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4083 Z= 0.191 Angle : 0.590 9.194 5515 Z= 0.315 Chirality : 0.039 0.207 623 Planarity : 0.004 0.060 689 Dihedral : 8.754 59.951 580 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.10 % Allowed : 26.94 % 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: 1.90 (0.37), residues: 496 helix: 1.95 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.43 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.007 0.001 TYR A 102 PHE 0.014 0.002 PHE B 60 TRP 0.006 0.001 TRP B 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 ( 4083) covalent geometry : angle 0.58953 / 0.31 ( 5515) hydrogen bonds : bond 0.05085 / 3.40 ( 334) hydrogen bonds : angle 4.39572 / 3.36 ( 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 86 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.142 Fit side-chains REVERT: A 47 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7255 (tmm-80) REVERT: A 197 VAL cc_start: 0.7084 (OUTLIER) cc_final: 0.6232 (p) REVERT: B 115 MET cc_start: 0.7226 (mmm) cc_final: 0.6705 (mmt) REVERT: B 200 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6955 (mp) REVERT: B 244 VAL cc_start: 0.7926 (p) cc_final: 0.7656 (t) outliers start: 21 outliers final: 9 residues processed: 83 average time/residue: 0.4082 time to fit residues: 35.2932 Evaluate side-chains 76 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 197 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 39 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.182555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.172228 restraints weight = 5861.851| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.72 r_work: 0.4289 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4083 Z= 0.149 Angle : 0.580 8.938 5515 Z= 0.302 Chirality : 0.038 0.195 623 Planarity : 0.004 0.046 689 Dihedral : 8.570 59.710 580 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 28.64 % Favored : 67.48 % 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: 2.21 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.38 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 87 TYR 0.008 0.001 TYR B 78 PHE 0.045 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/Z covalent geometry : bond 0.00301 / 0.15 ( 4083) covalent geometry : angle 0.58024 / 0.30 ( 5515) hydrogen bonds : bond 0.04644 / 3.12 ( 334) hydrogen bonds : angle 4.25083 / 3.26 ( 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 83 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.145 Fit side-chains REVERT: A 197 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6057 (p) REVERT: B 115 MET cc_start: 0.7206 (mmm) cc_final: 0.6794 (mmm) REVERT: B 200 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 281 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7213 (mt) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.3805 time to fit residues: 31.4053 Evaluate side-chains 78 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 91 VAL 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 106 THR 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 281 ILE 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: 0.5980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.180657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.170236 restraints weight = 5770.457| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 1.70 r_work: 0.4258 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3359 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= 0.184 Angle : 0.596 9.015 5515 Z= 0.315 Chirality : 0.039 0.218 623 Planarity : 0.004 0.033 689 Dihedral : 8.673 59.607 580 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.13 % Allowed : 29.61 % 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: 2.09 (0.37), residues: 496 helix: 2.12 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.47 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.010 0.001 TYR A 102 PHE 0.016 0.002 PHE B 60 TRP 0.006 0.001 TRP B 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 4083) covalent geometry : angle 0.59572 / 0.31 ( 5515) hydrogen bonds : bond 0.04959 / 3.32 ( 334) hydrogen bonds : angle 4.30801 / 3.30 ( 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 82 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.145 Fit side-chains REVERT: A 197 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6265 (p) REVERT: B 200 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6974 (mp) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 0.4219 time to fit residues: 35.2310 Evaluate side-chains 78 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 91 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.180463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.169993 restraints weight = 5845.365| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 1.71 r_work: 0.4253 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3396 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= 0.199 Angle : 0.634 9.233 5515 Z= 0.333 Chirality : 0.040 0.270 623 Planarity : 0.004 0.035 689 Dihedral : 8.753 59.619 580 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.64 % Allowed : 29.85 % 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: 1.92 (0.37), residues: 496 helix: 1.97 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.49 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.011 0.001 TYR B 130 PHE 0.025 0.002 PHE B 145 TRP 0.004 0.001 TRP B 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 ( 4083) covalent geometry : angle 0.63406 / 0.33 ( 5515) hydrogen bonds : bond 0.05073 / 3.40 ( 334) hydrogen bonds : angle 4.40765 / 3.37 ( 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 84 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.155 Fit side-chains REVERT: A 197 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6185 (p) REVERT: B 200 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7017 (mp) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.4622 time to fit residues: 39.4588 Evaluate side-chains 78 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 91 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.180252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.169809 restraints weight = 5732.976| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.70 r_work: 0.4256 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3516 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= 0.185 Angle : 0.631 9.373 5515 Z= 0.332 Chirality : 0.041 0.277 623 Planarity : 0.004 0.039 689 Dihedral : 8.726 59.565 580 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.40 % Allowed : 29.85 % Favored : 66.75 % 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: 1.90 (0.37), residues: 496 helix: 1.99 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.010 0.001 TYR B 130 PHE 0.046 0.002 PHE B 145 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 4083) covalent geometry : angle 0.63135 / 0.33 ( 5515) hydrogen bonds : bond 0.05032 / 3.39 ( 334) hydrogen bonds : angle 4.39431 / 3.36 ( 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 79 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.143 Fit side-chains REVERT: A 197 VAL cc_start: 0.7003 (OUTLIER) cc_final: 0.6137 (p) REVERT: B 200 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6968 (mp) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.3969 time to fit residues: 31.5447 Evaluate side-chains 78 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 197 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.179619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.168885 restraints weight = 5761.632| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.72 r_work: 0.4250 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4083 Z= 0.192 Angle : 0.629 9.382 5515 Z= 0.334 Chirality : 0.041 0.282 623 Planarity : 0.004 0.035 689 Dihedral : 8.762 59.222 580 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.64 % Allowed : 29.61 % Favored : 66.75 % 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: 1.83 (0.37), residues: 496 helix: 1.90 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.44 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 87 TYR 0.011 0.001 TYR B 130 PHE 0.066 0.002 PHE B 145 TRP 0.003 0.001 TRP A 95 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 4083) covalent geometry : angle 0.62863 / 0.33 ( 5515) hydrogen bonds : bond 0.05066 / 3.40 ( 334) hydrogen bonds : angle 4.41335 / 3.37 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.12 seconds wall clock time: 27 minutes 49.61 seconds (1669.61 seconds total)