Starting phenix.real_space_refine on Wed Mar 5 14:30:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4a_31705/03_2025/7v4a_31705.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1029 2.51 5 N 294 2.21 5 O 330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1653 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 551 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, B Time building chain proxies: 1.06, per 1000 atoms: 0.64 Number of scatterers: 1653 At special positions: 0 Unit cell: (67.84, 86.92, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 330 8.00 N 294 7.00 C 1029 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: 0.67 Conformation dependent library (CDL) restraints added in 200.2 milliseconds 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.702A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.620A pdb=" N THR A 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.604A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.744A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.729A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 91 30 hydrogen bonds defined for protein. 90 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: 0.38 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 291 1.29 - 1.36: 258 1.36 - 1.42: 51 1.42 - 1.48: 270 1.48 - 1.55: 786 Bond restraints: 1656 Sorted by residual: bond pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.63e-02 3.76e+03 9.11e-01 bond pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.63e-02 3.76e+03 8.64e-01 bond pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.63e-02 3.76e+03 7.79e-01 bond pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 1.516 1.502 0.014 2.50e-02 1.60e+03 3.35e-01 bond pdb=" CA GLN C 62 " pdb=" C GLN C 62 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.08e-02 8.57e+03 3.27e-01 ... (remaining 1651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 2047 0.89 - 1.79: 155 1.79 - 2.68: 12 2.68 - 3.58: 6 3.58 - 4.47: 3 Bond angle restraints: 2223 Sorted by residual: angle pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 5.00e+00 angle pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 4.99e+00 angle pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 angle pdb=" C GLU C 83 " pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 110.44 107.32 3.12 1.68e+00 3.54e-01 3.46e+00 angle pdb=" C GLU A 83 " pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 110.44 107.33 3.11 1.68e+00 3.54e-01 3.44e+00 ... (remaining 2218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 912 17.48 - 34.95: 45 34.95 - 52.42: 15 52.42 - 69.89: 3 69.89 - 87.37: 3 Dihedral angle restraints: 978 sinusoidal: 339 harmonic: 639 Sorted by residual: dihedral pdb=" CB GLU B 20 " pdb=" CG GLU B 20 " pdb=" CD GLU B 20 " pdb=" OE1 GLU B 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.37 -87.37 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU C 20 " pdb=" CG GLU C 20 " pdb=" CD GLU C 20 " pdb=" OE1 GLU C 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.36 -87.36 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 20 " pdb=" CG GLU A 20 " pdb=" CD GLU A 20 " pdb=" OE1 GLU A 20 " ideal model delta sinusoidal sigma weight residual 0.00 87.32 -87.32 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 134 0.026 - 0.052: 81 0.052 - 0.077: 22 0.077 - 0.103: 25 0.103 - 0.128: 23 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA VAL C 15 " pdb=" N VAL C 15 " pdb=" C VAL C 15 " pdb=" CB VAL C 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 282 not shown) Planarity restraints: 276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 83 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" CD GLU C 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU C 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU A 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 83 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CD GLU B 83 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU B 83 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 83 " 0.011 2.00e-02 2.50e+03 ... (remaining 273 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 667 2.92 - 3.41: 1441 3.41 - 3.91: 2358 3.91 - 4.40: 2385 4.40 - 4.90: 5063 Nonbonded interactions: 11914 Sorted by model distance: nonbonded pdb=" N ASP A 98 " pdb=" OD1 ASP A 98 " model vdw 2.423 3.120 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.423 3.120 nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.424 3.120 nonbonded pdb=" N GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.444 3.120 nonbonded pdb=" N GLU B 83 " pdb=" OE1 GLU B 83 " model vdw 2.445 3.120 ... (remaining 11909 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.200 Find NCS groups from input model: 0.030 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.002 0.016 1656 Z= 0.152 Angle : 0.518 4.471 2223 Z= 0.314 Chirality : 0.052 0.128 285 Planarity : 0.002 0.018 276 Dihedral : 14.278 87.365 576 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.80 (0.26), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.20), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.001 0.000 PHE C 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.175 Fit side-chains REVERT: A 21 LYS cc_start: 0.9387 (tttm) cc_final: 0.9148 (tttt) REVERT: A 58 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7898 (tptp) REVERT: A 60 LYS cc_start: 0.8623 (mmtp) cc_final: 0.7923 (mttp) REVERT: A 80 LYS cc_start: 0.8612 (mttp) cc_final: 0.7335 (pttp) REVERT: A 97 LYS cc_start: 0.8710 (ptmm) cc_final: 0.7552 (tppt) REVERT: B 20 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 46 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 58 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8094 (tppt) REVERT: B 59 THR cc_start: 0.9172 (m) cc_final: 0.8882 (t) REVERT: B 60 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7959 (mmtm) REVERT: C 23 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8426 (mmmt) REVERT: C 45 LYS cc_start: 0.8431 (tttp) cc_final: 0.8186 (ttpt) REVERT: C 46 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 58 LYS cc_start: 0.8656 (ttmm) cc_final: 0.7995 (pttm) REVERT: C 60 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7750 (mttm) REVERT: C 61 GLU cc_start: 0.8071 (mp0) cc_final: 0.7596 (mp0) REVERT: C 80 LYS cc_start: 0.8339 (mttp) cc_final: 0.7649 (mmtt) REVERT: C 83 GLU cc_start: 0.5457 (mp0) cc_final: 0.4921 (mp0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2128 time to fit residues: 16.5221 Evaluate side-chains 58 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106811 restraints weight = 2287.331| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.32 r_work: 0.3479 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 1656 Z= 0.438 Angle : 0.608 3.796 2223 Z= 0.360 Chirality : 0.051 0.132 285 Planarity : 0.003 0.011 276 Dihedral : 5.660 19.677 237 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 4.85 % Allowed : 21.21 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.30), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.23), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.005 0.001 PHE B 94 TYR 0.015 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.166 Fit side-chains REVERT: A 24 GLN cc_start: 0.8828 (mm110) cc_final: 0.8300 (mp10) REVERT: A 58 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8178 (tptp) REVERT: A 60 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8262 (mttp) REVERT: A 80 LYS cc_start: 0.8926 (mttp) cc_final: 0.7578 (pttp) REVERT: A 97 LYS cc_start: 0.8708 (ptmm) cc_final: 0.7306 (tppt) REVERT: B 20 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8597 (mt-10) REVERT: B 46 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 23 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8504 (mmmt) REVERT: C 45 LYS cc_start: 0.8445 (tttp) cc_final: 0.8200 (ttpt) REVERT: C 46 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 58 LYS cc_start: 0.8646 (ttmm) cc_final: 0.7932 (pttm) REVERT: C 60 LYS cc_start: 0.8596 (mmtp) cc_final: 0.6560 (pttm) REVERT: C 61 GLU cc_start: 0.8498 (mp0) cc_final: 0.8019 (mp0) REVERT: C 80 LYS cc_start: 0.8818 (mttp) cc_final: 0.8084 (mmtt) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1844 time to fit residues: 12.7536 Evaluate side-chains 62 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.141338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112510 restraints weight = 2275.345| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.41 r_work: 0.3579 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1656 Z= 0.200 Angle : 0.479 2.718 2223 Z= 0.283 Chirality : 0.049 0.127 285 Planarity : 0.002 0.007 276 Dihedral : 4.737 15.469 237 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 6.06 % Allowed : 18.79 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.33), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.190 Fit side-chains REVERT: A 24 GLN cc_start: 0.8755 (mm110) cc_final: 0.8211 (mp10) REVERT: A 58 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8068 (tptp) REVERT: A 60 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8083 (mttp) REVERT: A 61 GLU cc_start: 0.8449 (mp0) cc_final: 0.8125 (mp0) REVERT: A 97 LYS cc_start: 0.8608 (ptmm) cc_final: 0.7245 (tppt) REVERT: B 20 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8612 (mt-10) REVERT: B 46 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 23 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8506 (mmmt) REVERT: C 46 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 58 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8032 (pttm) REVERT: C 60 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8084 (mmtm) REVERT: C 61 GLU cc_start: 0.8413 (mp0) cc_final: 0.7959 (mp0) REVERT: C 80 LYS cc_start: 0.8780 (mttp) cc_final: 0.7950 (mmtt) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.1694 time to fit residues: 11.4380 Evaluate side-chains 58 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.139246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110441 restraints weight = 2233.349| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.42 r_work: 0.3588 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1656 Z= 0.265 Angle : 0.487 2.928 2223 Z= 0.288 Chirality : 0.049 0.126 285 Planarity : 0.002 0.008 276 Dihedral : 4.889 15.279 237 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 10.30 % Allowed : 17.58 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.33), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.25), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.179 Fit side-chains REVERT: A 23 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8192 (mtpt) REVERT: A 24 GLN cc_start: 0.8788 (mm110) cc_final: 0.8242 (mp10) REVERT: A 58 LYS cc_start: 0.8606 (ttmm) cc_final: 0.7963 (tptt) REVERT: A 60 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8027 (mttp) REVERT: A 61 GLU cc_start: 0.8486 (mp0) cc_final: 0.8153 (mp0) REVERT: A 80 LYS cc_start: 0.8942 (mttp) cc_final: 0.7598 (pttp) REVERT: A 97 LYS cc_start: 0.8630 (ptmm) cc_final: 0.7244 (tppt) REVERT: B 20 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 46 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 57 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: C 23 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8497 (mmmt) REVERT: C 46 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 58 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8066 (pttm) REVERT: C 60 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8088 (mmtm) REVERT: C 61 GLU cc_start: 0.8429 (mp0) cc_final: 0.7969 (mp0) REVERT: C 80 LYS cc_start: 0.8815 (mttp) cc_final: 0.8019 (mmtt) outliers start: 17 outliers final: 13 residues processed: 66 average time/residue: 0.1688 time to fit residues: 12.3262 Evaluate side-chains 67 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116636 restraints weight = 2182.590| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.18 r_work: 0.3626 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1656 Z= 0.164 Angle : 0.444 3.125 2223 Z= 0.262 Chirality : 0.049 0.127 285 Planarity : 0.002 0.008 276 Dihedral : 4.497 14.960 237 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 8.48 % Allowed : 18.79 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.189 Fit side-chains REVERT: A 23 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8167 (mtpt) REVERT: A 24 GLN cc_start: 0.8696 (mm110) cc_final: 0.8233 (mp10) REVERT: A 58 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8088 (tptp) REVERT: A 61 GLU cc_start: 0.8402 (mp0) cc_final: 0.8136 (mp0) REVERT: A 97 LYS cc_start: 0.8629 (ptmm) cc_final: 0.7272 (tppt) REVERT: B 20 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 46 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7169 (tm-30) REVERT: C 23 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8487 (mmmt) REVERT: C 46 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7529 (tm-30) REVERT: C 58 LYS cc_start: 0.8689 (ttmm) cc_final: 0.7958 (pttm) REVERT: C 60 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8090 (mmtm) REVERT: C 61 GLU cc_start: 0.8371 (mp0) cc_final: 0.7901 (mp0) REVERT: C 80 LYS cc_start: 0.8774 (mttp) cc_final: 0.7971 (mmtt) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.1712 time to fit residues: 11.8011 Evaluate side-chains 62 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.139724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111594 restraints weight = 2240.025| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.22 r_work: 0.3582 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1656 Z= 0.230 Angle : 0.468 2.957 2223 Z= 0.277 Chirality : 0.049 0.127 285 Planarity : 0.002 0.007 276 Dihedral : 4.694 15.035 237 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 9.70 % Allowed : 20.00 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.189 Fit side-chains REVERT: A 61 GLU cc_start: 0.8441 (mp0) cc_final: 0.8162 (mp0) REVERT: B 20 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8575 (mt-10) REVERT: B 46 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 57 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: C 23 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8488 (mmmt) REVERT: C 46 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 58 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8013 (pttm) REVERT: C 60 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8140 (mmtm) REVERT: C 61 GLU cc_start: 0.8394 (mp0) cc_final: 0.7949 (mp0) REVERT: C 80 LYS cc_start: 0.8819 (mttp) cc_final: 0.8036 (mmtt) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 0.1400 time to fit residues: 9.5707 Evaluate side-chains 60 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111124 restraints weight = 2234.316| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.25 r_work: 0.3583 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1656 Z= 0.254 Angle : 0.487 3.183 2223 Z= 0.288 Chirality : 0.049 0.127 285 Planarity : 0.002 0.010 276 Dihedral : 4.838 15.264 237 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 10.30 % Allowed : 18.79 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.004 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.200 Fit side-chains REVERT: A 24 GLN cc_start: 0.8414 (mp10) cc_final: 0.7938 (mp10) REVERT: A 61 GLU cc_start: 0.8412 (mp0) cc_final: 0.8150 (mp0) REVERT: A 80 LYS cc_start: 0.8942 (mttp) cc_final: 0.7623 (pttp) REVERT: B 20 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8539 (mt-10) REVERT: B 46 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7225 (tm-30) REVERT: B 57 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: C 23 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8510 (mmmt) REVERT: C 46 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7517 (tm-30) REVERT: C 58 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8053 (pttm) REVERT: C 60 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8090 (mmtm) REVERT: C 61 GLU cc_start: 0.8360 (mp0) cc_final: 0.7908 (mp0) REVERT: C 80 LYS cc_start: 0.8829 (mttp) cc_final: 0.8063 (mmtt) outliers start: 17 outliers final: 14 residues processed: 60 average time/residue: 0.1423 time to fit residues: 9.6909 Evaluate side-chains 64 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.136211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108299 restraints weight = 2259.757| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.28 r_work: 0.3555 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1656 Z= 0.337 Angle : 0.537 3.662 2223 Z= 0.317 Chirality : 0.050 0.129 285 Planarity : 0.002 0.011 276 Dihedral : 5.136 15.441 237 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 9.70 % Allowed : 18.79 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.35), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.27), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.004 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.178 Fit side-chains REVERT: A 23 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8401 (mtpt) REVERT: A 24 GLN cc_start: 0.8501 (mp10) cc_final: 0.8032 (mp10) REVERT: A 58 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8063 (tptp) REVERT: A 60 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8138 (mttm) REVERT: A 61 GLU cc_start: 0.8449 (mp0) cc_final: 0.8159 (mp0) REVERT: A 80 LYS cc_start: 0.8983 (mttp) cc_final: 0.7761 (pttp) REVERT: A 97 LYS cc_start: 0.8671 (ptmm) cc_final: 0.7309 (tppt) REVERT: B 20 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8575 (mt-10) REVERT: B 46 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 57 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: B 83 GLU cc_start: 0.6734 (mp0) cc_final: 0.6196 (mp0) REVERT: C 23 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8468 (mmmt) REVERT: C 46 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 58 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7995 (pttm) REVERT: C 60 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8122 (mmtm) REVERT: C 61 GLU cc_start: 0.8432 (mp0) cc_final: 0.7994 (mp0) REVERT: C 80 LYS cc_start: 0.8870 (mttp) cc_final: 0.8150 (mmtt) outliers start: 16 outliers final: 15 residues processed: 66 average time/residue: 0.1621 time to fit residues: 11.8444 Evaluate side-chains 71 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.141828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113355 restraints weight = 2242.920| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.35 r_work: 0.3592 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1656 Z= 0.213 Angle : 0.484 3.881 2223 Z= 0.285 Chirality : 0.049 0.129 285 Planarity : 0.002 0.013 276 Dihedral : 4.818 15.391 237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 8.48 % Allowed : 20.00 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.28), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.187 Fit side-chains REVERT: A 23 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8385 (mtpt) REVERT: A 24 GLN cc_start: 0.8446 (mp10) cc_final: 0.7973 (mp10) REVERT: A 58 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7996 (tptp) REVERT: A 60 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8057 (mttm) REVERT: A 61 GLU cc_start: 0.8428 (mp0) cc_final: 0.8130 (mp0) REVERT: A 80 LYS cc_start: 0.8923 (mttp) cc_final: 0.7556 (pttp) REVERT: A 97 LYS cc_start: 0.8535 (ptmm) cc_final: 0.7222 (tppt) REVERT: B 20 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8532 (mt-10) REVERT: B 46 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 57 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: C 23 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8447 (mmmt) REVERT: C 46 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 58 LYS cc_start: 0.8714 (ttmm) cc_final: 0.7944 (pttm) REVERT: C 60 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8091 (mmtm) REVERT: C 61 GLU cc_start: 0.8384 (mp0) cc_final: 0.7931 (mp0) REVERT: C 80 LYS cc_start: 0.8822 (mttp) cc_final: 0.8029 (mmtt) outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.1728 time to fit residues: 12.4229 Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.138051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109914 restraints weight = 2313.908| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.35 r_work: 0.3571 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1656 Z= 0.258 Angle : 0.501 3.558 2223 Z= 0.295 Chirality : 0.050 0.129 285 Planarity : 0.002 0.012 276 Dihedral : 4.892 15.289 237 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 9.09 % Allowed : 20.00 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.28), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 456 Ramachandran restraints generated. 228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.188 Fit side-chains REVERT: A 23 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8468 (mtpt) REVERT: A 24 GLN cc_start: 0.8500 (mp10) cc_final: 0.8090 (mp10) REVERT: A 58 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8001 (tptp) REVERT: A 60 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8102 (mttm) REVERT: A 61 GLU cc_start: 0.8469 (mp0) cc_final: 0.8194 (mp0) REVERT: A 80 LYS cc_start: 0.8952 (mttp) cc_final: 0.7591 (pttp) REVERT: A 97 LYS cc_start: 0.8637 (ptmm) cc_final: 0.7301 (tppt) REVERT: B 20 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 46 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 57 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: C 23 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8460 (mmmt) REVERT: C 46 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 58 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8073 (pttm) REVERT: C 60 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8102 (mmtm) REVERT: C 61 GLU cc_start: 0.8406 (mp0) cc_final: 0.7972 (mp0) REVERT: C 80 LYS cc_start: 0.8842 (mttp) cc_final: 0.8059 (mmtt) outliers start: 15 outliers final: 14 residues processed: 65 average time/residue: 0.1659 time to fit residues: 11.9533 Evaluate side-chains 69 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112965 restraints weight = 2278.539| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.31 r_work: 0.3580 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1656 Z= 0.263 Angle : 0.507 4.053 2223 Z= 0.298 Chirality : 0.050 0.129 285 Planarity : 0.002 0.014 276 Dihedral : 4.930 15.240 237 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 10.30 % Allowed : 18.79 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.28), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.012 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1279.54 seconds wall clock time: 23 minutes 18.37 seconds (1398.37 seconds total)