Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_31705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_31705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_31705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_31705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4a_31705/03_2024/7v4a_31705.pdb" } 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 Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1653 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 1.29, per 1000 atoms: 0.78 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 290.2 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: 0.24 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: 0.37 Time building geometry restraints manager: 0.65 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: 106.09 - 111.12: 677 111.12 - 116.15: 534 116.15 - 121.18: 463 121.18 - 126.21: 546 126.21 - 131.24: 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 2.520 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.423 2.520 nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.424 2.520 nonbonded pdb=" N GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.444 2.520 nonbonded pdb=" N GLU B 83 " pdb=" OE1 GLU B 83 " model vdw 2.445 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.990 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: 4.560 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.120 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.194 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: 0.2242 time to fit residues: 17.4487 Evaluate side-chains 58 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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: 5.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1656 Z= 0.271 Angle : 0.510 4.196 2223 Z= 0.301 Chirality : 0.050 0.126 285 Planarity : 0.002 0.011 276 Dihedral : 4.910 14.894 237 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 6.06 % Allowed : 21.21 % 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: -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 0.004 0.001 PHE B 94 TYR 0.014 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 71 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.189 Fit side-chains REVERT: A 24 GLN cc_start: 0.8840 (mm110) cc_final: 0.8400 (mp10) REVERT: A 58 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7834 (tptt) REVERT: A 60 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8112 (mttp) REVERT: A 61 GLU cc_start: 0.8114 (mp0) cc_final: 0.7869 (mp0) REVERT: A 80 LYS cc_start: 0.8711 (mttp) cc_final: 0.7401 (pttp) REVERT: A 97 LYS cc_start: 0.8831 (ptmm) cc_final: 0.7499 (tppt) REVERT: B 20 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 46 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6990 (tm-30) REVERT: C 23 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8486 (mmmt) REVERT: C 46 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7092 (tm-30) REVERT: C 58 LYS cc_start: 0.8659 (ttmm) cc_final: 0.7990 (pttm) REVERT: C 60 LYS cc_start: 0.8597 (mmtp) cc_final: 0.6573 (pttm) REVERT: C 61 GLU cc_start: 0.8126 (mp0) cc_final: 0.7658 (mp0) REVERT: C 80 LYS cc_start: 0.8596 (mttp) cc_final: 0.7957 (mmtt) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.1749 time to fit residues: 12.3057 Evaluate side-chains 61 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 44 THR 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 19 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1656 Z= 0.206 Angle : 0.447 2.510 2223 Z= 0.264 Chirality : 0.049 0.127 285 Planarity : 0.002 0.007 276 Dihedral : 4.487 14.958 237 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 6.67 % Allowed : 23.03 % 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: -5.13 (0.32), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.24), 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 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 66 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.186 Fit side-chains REVERT: A 58 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7872 (tptt) REVERT: A 60 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7905 (mttp) REVERT: A 97 LYS cc_start: 0.8813 (ptmm) cc_final: 0.7467 (tppt) REVERT: B 20 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 46 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6767 (tm-30) REVERT: C 23 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8528 (mmmt) REVERT: C 58 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8037 (pttm) REVERT: C 60 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8117 (mmtm) REVERT: C 61 GLU cc_start: 0.8096 (mp0) cc_final: 0.7658 (mp0) REVERT: C 80 LYS cc_start: 0.8672 (mttp) cc_final: 0.7909 (mmtt) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.1602 time to fit residues: 10.6503 Evaluate side-chains 63 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 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 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1656 Z= 0.218 Angle : 0.453 3.412 2223 Z= 0.267 Chirality : 0.049 0.125 285 Planarity : 0.002 0.012 276 Dihedral : 4.597 15.366 237 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 11.52 % Allowed : 19.39 % Favored : 69.09 % 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: -5.01 (0.33), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (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 74 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.182 Fit side-chains REVERT: A 23 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8044 (mtpt) REVERT: A 24 GLN cc_start: 0.8459 (mp10) cc_final: 0.7966 (mp10) REVERT: A 58 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7955 (tptt) REVERT: A 80 LYS cc_start: 0.8789 (mttp) cc_final: 0.7514 (pttp) REVERT: A 97 LYS cc_start: 0.8846 (ptmm) cc_final: 0.7459 (tppt) REVERT: B 20 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 46 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 23 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8508 (mmmt) REVERT: C 58 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7936 (pttm) REVERT: C 60 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8077 (mmtm) REVERT: C 61 GLU cc_start: 0.8133 (mp0) cc_final: 0.7692 (mp0) REVERT: C 80 LYS cc_start: 0.8679 (mttp) cc_final: 0.7927 (mmtt) outliers start: 19 outliers final: 15 residues processed: 65 average time/residue: 0.1610 time to fit residues: 11.6262 Evaluate side-chains 68 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 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 87 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 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 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1656 Z= 0.186 Angle : 0.430 2.273 2223 Z= 0.255 Chirality : 0.048 0.127 285 Planarity : 0.002 0.006 276 Dihedral : 4.396 15.245 237 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 9.70 % Allowed : 21.21 % Favored : 69.09 % 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: -4.85 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.26), 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 0.010 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 fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.188 Fit side-chains REVERT: A 58 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8045 (tptp) REVERT: A 97 LYS cc_start: 0.8823 (ptmm) cc_final: 0.7473 (tppt) REVERT: B 20 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 46 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6767 (tm-30) REVERT: C 23 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8514 (mmmt) REVERT: C 58 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8018 (pttm) REVERT: C 60 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8094 (mmtm) REVERT: C 61 GLU cc_start: 0.8130 (mp0) cc_final: 0.7708 (mp0) REVERT: C 80 LYS cc_start: 0.8677 (mttp) cc_final: 0.7922 (mmtt) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 0.1496 time to fit residues: 10.0293 Evaluate side-chains 63 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1656 Z= 0.248 Angle : 0.464 3.031 2223 Z= 0.274 Chirality : 0.049 0.127 285 Planarity : 0.002 0.013 276 Dihedral : 4.641 15.368 237 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 12.12 % Allowed : 18.79 % Favored : 69.09 % 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: -4.76 (0.34), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.26), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 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 73 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.183 Fit side-chains REVERT: A 58 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7976 (tptt) REVERT: A 80 LYS cc_start: 0.8790 (mttp) cc_final: 0.7559 (pttp) REVERT: A 97 LYS cc_start: 0.8824 (ptmm) cc_final: 0.7481 (tppt) REVERT: B 20 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 46 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6796 (tm-30) REVERT: C 23 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8511 (mmmt) REVERT: C 58 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7942 (pttm) REVERT: C 60 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8098 (mmtm) REVERT: C 61 GLU cc_start: 0.8149 (mp0) cc_final: 0.7730 (mp0) REVERT: C 80 LYS cc_start: 0.8716 (mttp) cc_final: 0.7949 (mmtt) outliers start: 20 outliers final: 17 residues processed: 65 average time/residue: 0.1580 time to fit residues: 11.3609 Evaluate side-chains 69 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 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 B residue 98 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1656 Z= 0.159 Angle : 0.410 2.238 2223 Z= 0.243 Chirality : 0.048 0.127 285 Planarity : 0.002 0.008 276 Dihedral : 4.309 14.933 237 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 9.70 % Allowed : 21.21 % Favored : 69.09 % 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: -4.60 (0.36), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.003 0.001 PHE B 94 TYR 0.009 0.001 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 70 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.196 Fit side-chains REVERT: A 24 GLN cc_start: 0.8456 (mp10) cc_final: 0.8004 (mp10) REVERT: A 58 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8030 (tptp) REVERT: A 97 LYS cc_start: 0.8795 (ptmm) cc_final: 0.7487 (tppt) REVERT: B 20 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 46 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6902 (tm-30) REVERT: C 23 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8508 (mmmt) REVERT: C 58 LYS cc_start: 0.8497 (ttmm) cc_final: 0.7948 (pttm) REVERT: C 60 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8045 (mmtm) REVERT: C 61 GLU cc_start: 0.8131 (mp0) cc_final: 0.7706 (mp0) REVERT: C 80 LYS cc_start: 0.8674 (mttp) cc_final: 0.7925 (mmtt) outliers start: 16 outliers final: 15 residues processed: 63 average time/residue: 0.1607 time to fit residues: 11.2592 Evaluate side-chains 66 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 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 87 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 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 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1656 Z= 0.096 Angle : 0.387 3.668 2223 Z= 0.228 Chirality : 0.049 0.125 285 Planarity : 0.002 0.013 276 Dihedral : 3.862 14.343 237 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 7.27 % Allowed : 23.64 % Favored : 69.09 % 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: -4.29 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.30), 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 0.009 0.001 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 69 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.196 Fit side-chains REVERT: A 24 GLN cc_start: 0.8448 (mp10) cc_final: 0.7987 (mp10) REVERT: B 20 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 46 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6867 (tm-30) REVERT: C 23 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8472 (mmmt) REVERT: C 58 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8024 (pttm) REVERT: C 60 LYS cc_start: 0.8624 (mmtp) cc_final: 0.7904 (tptt) REVERT: C 61 GLU cc_start: 0.8087 (mp0) cc_final: 0.7650 (mp0) REVERT: C 80 LYS cc_start: 0.8584 (mttp) cc_final: 0.7843 (mmtt) REVERT: C 97 LYS cc_start: 0.8775 (ptmm) cc_final: 0.8510 (ptmt) outliers start: 12 outliers final: 12 residues processed: 63 average time/residue: 0.1621 time to fit residues: 11.2642 Evaluate side-chains 63 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 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 81 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 44 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2680 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 : 0.437 6.588 2223 Z= 0.256 Chirality : 0.049 0.126 285 Planarity : 0.002 0.012 276 Dihedral : 4.080 14.469 237 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.48 % Allowed : 26.06 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.27 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.001 PHE B 94 TYR 0.009 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 65 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.184 Fit side-chains REVERT: A 24 GLN cc_start: 0.8454 (mp10) cc_final: 0.8004 (mp10) REVERT: B 20 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 46 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6953 (tm-30) REVERT: C 23 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8490 (mmmt) REVERT: C 58 LYS cc_start: 0.8488 (ttmm) cc_final: 0.7952 (pttm) REVERT: C 60 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8042 (tptt) REVERT: C 61 GLU cc_start: 0.8129 (mp0) cc_final: 0.7663 (mp0) REVERT: C 80 LYS cc_start: 0.8646 (mttp) cc_final: 0.7923 (mmtt) REVERT: C 97 LYS cc_start: 0.8808 (ptmm) cc_final: 0.8589 (ptmt) outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 0.1157 time to fit residues: 7.8014 Evaluate side-chains 63 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 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 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR 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 19 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1656 Z= 0.280 Angle : 0.524 6.283 2223 Z= 0.306 Chirality : 0.049 0.127 285 Planarity : 0.002 0.017 276 Dihedral : 4.712 14.520 237 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 7.88 % Allowed : 26.06 % Favored : 66.06 % 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: -4.39 (0.38), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.29), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.010 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 65 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.197 Fit side-chains REVERT: A 80 LYS cc_start: 0.8799 (mttp) cc_final: 0.7552 (pttp) REVERT: B 20 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 46 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6990 (tm-30) REVERT: C 23 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8480 (mmmt) REVERT: C 58 LYS cc_start: 0.8428 (ttmm) cc_final: 0.7923 (pttm) REVERT: C 60 LYS cc_start: 0.8596 (mmtp) cc_final: 0.7986 (tptt) REVERT: C 61 GLU cc_start: 0.8125 (mp0) cc_final: 0.7676 (mp0) REVERT: C 80 LYS cc_start: 0.8720 (mttp) cc_final: 0.7975 (mmtt) outliers start: 13 outliers final: 12 residues processed: 59 average time/residue: 0.1394 time to fit residues: 9.2797 Evaluate side-chains 64 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 C residue 44 THR Chi-restraints excluded: chain C residue 72 THR 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 13 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.143615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.115064 restraints weight = 2185.921| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.30 r_work: 0.3641 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1656 Z= 0.149 Angle : 0.445 6.413 2223 Z= 0.261 Chirality : 0.049 0.127 285 Planarity : 0.002 0.013 276 Dihedral : 4.272 14.726 237 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 7.27 % Allowed : 24.24 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.26 (0.39), residues: 228 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.30), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.002 0.001 PHE B 94 TYR 0.010 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1023.69 seconds wall clock time: 19 minutes 43.44 seconds (1183.44 seconds total)