Starting phenix.real_space_refine on Thu Sep 26 22:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/09_2024/6n2p_9332.cif" } resolution = 4.0 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= -0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 4630 2.51 5 N 1210 2.21 5 O 1330 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "B" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "C" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "D" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "E" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "G" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "H" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "J" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Time building chain proxies: 7.57, per 1000 atoms: 0.52 Number of scatterers: 14570 At special positions: 0 Unit cell: (91.14, 91.14, 87.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1330 8.00 N 1210 7.00 C 4630 6.00 H 7380 1.00 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: 4.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Proline residue: B 32 - end of helix Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 87 through 95 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 18 through 25 Processing helix chain 'E' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Proline residue: E 32 - end of helix Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 18 through 25 Processing helix chain 'G' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 41 through 50 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 Processing helix chain 'G' and resid 87 through 95 Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 41 through 50 Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 87 Processing helix chain 'H' and resid 87 through 95 Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 18 through 25 Processing helix chain 'I' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Proline residue: I 32 - end of helix Processing helix chain 'I' and resid 41 through 50 Processing helix chain 'I' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 87 Processing helix chain 'I' and resid 87 through 95 Processing helix chain 'J' and resid 10 through 15 Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE J 30 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Proline residue: J 32 - end of helix Processing helix chain 'J' and resid 41 through 50 Processing helix chain 'J' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 87 Processing helix chain 'J' and resid 87 through 95 420 hydrogen bonds defined for protein. 1260 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: 4.52 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7360 1.03 - 1.23: 20 1.23 - 1.42: 2950 1.42 - 1.62: 4360 1.62 - 1.81: 20 Bond restraints: 14710 Sorted by residual: bond pdb=" CG LEU H 65 " pdb=" CD1 LEU H 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU J 65 " pdb=" CD1 LEU J 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU G 65 " pdb=" CD1 LEU G 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU E 65 " pdb=" CD1 LEU E 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU I 65 " pdb=" CD1 LEU I 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 14705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 24237 1.27 - 2.53: 2236 2.53 - 3.80: 217 3.80 - 5.07: 20 5.07 - 6.34: 30 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C GLN C 36 " pdb=" N CYS C 37 " pdb=" CA CYS C 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN F 36 " pdb=" N CYS F 37 " pdb=" CA CYS F 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN E 36 " pdb=" N CYS E 37 " pdb=" CA CYS E 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN A 36 " pdb=" N CYS A 37 " pdb=" CA CYS A 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN B 36 " pdb=" N CYS B 37 " pdb=" CA CYS B 37 " ideal model delta sigma weight residual 122.31 116.69 5.62 2.00e+00 2.50e-01 7.91e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.88: 6381 11.88 - 23.77: 259 23.77 - 35.65: 100 35.65 - 47.53: 70 47.53 - 59.41: 30 Dihedral angle restraints: 6840 sinusoidal: 3850 harmonic: 2990 Sorted by residual: dihedral pdb=" CA LEU E 54 " pdb=" C LEU E 54 " pdb=" N VAL E 55 " pdb=" CA VAL E 55 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU F 54 " pdb=" C LEU F 54 " pdb=" N VAL F 55 " pdb=" CA VAL F 55 " ideal model delta harmonic sigma weight residual -180.00 -163.95 -16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA LEU J 54 " pdb=" C LEU J 54 " pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 529 0.025 - 0.050: 353 0.050 - 0.075: 192 0.075 - 0.100: 46 0.100 - 0.125: 40 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA PRO J 32 " pdb=" N PRO J 32 " pdb=" C PRO J 32 " pdb=" CB PRO J 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA PRO C 52 " pdb=" N PRO C 52 " pdb=" C PRO C 52 " pdb=" CB PRO C 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1157 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 51 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 51 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO D 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 51 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO I 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 52 " -0.030 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 817 2.19 - 2.79: 30538 2.79 - 3.39: 36506 3.39 - 4.00: 45180 4.00 - 4.60: 72363 Nonbonded interactions: 185404 Sorted by model distance: nonbonded pdb="HD22 ASN D 53 " pdb=" O PRO E 52 " model vdw 1.586 2.450 nonbonded pdb=" OE2 GLU B 15 " pdb=" HE ARG E 35 " model vdw 1.589 2.450 nonbonded pdb=" OE2 GLU C 15 " pdb=" HE ARG F 35 " model vdw 1.596 2.450 nonbonded pdb=" HE ARG B 35 " pdb=" OE2 GLU H 15 " model vdw 1.601 2.450 nonbonded pdb="HD22 ASN E 53 " pdb=" O PRO F 52 " model vdw 1.621 2.450 ... (remaining 185399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.270 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.009 0.046 7330 Z= 0.615 Angle : 0.872 6.337 9950 Z= 0.466 Chirality : 0.043 0.125 1160 Planarity : 0.007 0.055 1250 Dihedral : 7.864 35.860 2810 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -4.67 (0.22), residues: 860 helix: -2.30 (0.16), residues: 670 sheet: None (None), residues: 0 loop : -5.46 (0.22), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 11 HIS 0.004 0.003 HIS G 73 PHE 0.013 0.004 PHE J 79 TYR 0.004 0.001 TYR D 87 ARG 0.003 0.001 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.7564 time to fit residues: 105.5354 Evaluate side-chains 56 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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: 0.7617 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7330 Z= 0.210 Angle : 0.624 4.601 9950 Z= 0.330 Chirality : 0.036 0.106 1160 Planarity : 0.006 0.045 1250 Dihedral : 5.044 14.656 980 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.12 % Allowed : 8.31 % Favored : 91.57 % 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: -2.39 (0.27), residues: 860 helix: -0.50 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -5.41 (0.23), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 11 HIS 0.001 0.000 HIS E 73 PHE 0.007 0.001 PHE E 17 TYR 0.010 0.001 TYR F 87 ARG 0.005 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASP cc_start: 0.7916 (p0) cc_final: 0.7615 (p0) REVERT: G 43 ASP cc_start: 0.7612 (p0) cc_final: 0.7131 (p0) REVERT: H 43 ASP cc_start: 0.7500 (p0) cc_final: 0.7039 (p0) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.4606 time to fit residues: 39.9789 Evaluate side-chains 44 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 7330 Z= 0.386 Angle : 0.681 4.902 9950 Z= 0.367 Chirality : 0.036 0.110 1160 Planarity : 0.005 0.032 1250 Dihedral : 5.196 15.047 980 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 0.48 % Allowed : 8.07 % Favored : 91.45 % 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: -1.78 (0.28), residues: 860 helix: -0.22 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.74 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 11 HIS 0.002 0.001 HIS A 73 PHE 0.005 0.001 PHE D 79 TYR 0.014 0.002 TYR D 87 ARG 0.005 0.001 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.4963 time to fit residues: 24.9871 Evaluate side-chains 28 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7330 Z= 0.255 Angle : 0.588 4.930 9950 Z= 0.309 Chirality : 0.036 0.109 1160 Planarity : 0.004 0.030 1250 Dihedral : 4.837 15.432 980 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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: -1.03 (0.28), residues: 860 helix: 0.31 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.52 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 11 HIS 0.001 0.000 HIS B 73 PHE 0.004 0.001 PHE G 17 TYR 0.007 0.001 TYR D 87 ARG 0.005 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.5807 time to fit residues: 19.2630 Evaluate side-chains 19 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7330 Z= 0.212 Angle : 0.550 4.685 9950 Z= 0.288 Chirality : 0.035 0.104 1160 Planarity : 0.004 0.031 1250 Dihedral : 4.635 15.261 980 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.29), residues: 860 helix: 0.73 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.22 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 11 HIS 0.001 0.000 HIS C 73 PHE 0.003 0.001 PHE H 17 TYR 0.009 0.001 TYR I 87 ARG 0.004 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.4269 time to fit residues: 14.4814 Evaluate side-chains 19 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7330 Z= 0.136 Angle : 0.515 4.570 9950 Z= 0.262 Chirality : 0.035 0.106 1160 Planarity : 0.003 0.029 1250 Dihedral : 4.302 14.692 980 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.30), residues: 860 helix: 1.18 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.86 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 11 HIS 0.001 0.000 HIS B 73 PHE 0.003 0.001 PHE E 17 TYR 0.005 0.001 TYR I 86 ARG 0.002 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3412 time to fit residues: 14.2488 Evaluate side-chains 16 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7330 Z= 0.282 Angle : 0.574 4.468 9950 Z= 0.306 Chirality : 0.036 0.109 1160 Planarity : 0.004 0.055 1250 Dihedral : 4.680 15.465 980 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.29), residues: 860 helix: 0.88 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.12 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 11 HIS 0.002 0.001 HIS J 73 PHE 0.003 0.001 PHE G 17 TYR 0.007 0.001 TYR I 87 ARG 0.007 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.3550 time to fit residues: 10.2525 Evaluate side-chains 15 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7330 Z= 0.186 Angle : 0.529 4.497 9950 Z= 0.276 Chirality : 0.035 0.106 1160 Planarity : 0.004 0.050 1250 Dihedral : 4.495 14.959 980 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.12 % Allowed : 8.67 % Favored : 91.20 % 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: 0.11 (0.29), residues: 860 helix: 1.01 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -3.92 (0.36), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 11 HIS 0.001 0.000 HIS D 73 PHE 0.003 0.000 PHE G 17 TYR 0.005 0.001 TYR I 87 ARG 0.005 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.2839 time to fit residues: 9.5589 Evaluate side-chains 15 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7330 Z= 0.143 Angle : 0.508 4.506 9950 Z= 0.261 Chirality : 0.035 0.106 1160 Planarity : 0.003 0.048 1250 Dihedral : 4.335 15.053 980 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.12 % Allowed : 8.80 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.30), residues: 860 helix: 1.26 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -3.84 (0.36), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 11 HIS 0.000 0.000 HIS D 73 PHE 0.003 0.001 PHE G 17 TYR 0.004 0.001 TYR I 86 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.2530 time to fit residues: 8.3516 Evaluate side-chains 13 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7330 Z= 0.168 Angle : 0.517 4.961 9950 Z= 0.269 Chirality : 0.035 0.105 1160 Planarity : 0.003 0.049 1250 Dihedral : 4.382 14.667 980 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.12 % Allowed : 9.04 % Favored : 90.84 % 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: 0.43 (0.30), residues: 860 helix: 1.24 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -3.82 (0.36), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 11 HIS 0.001 0.000 HIS J 73 PHE 0.002 0.000 PHE G 17 TYR 0.004 0.001 TYR I 87 ARG 0.006 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.2649 time to fit residues: 7.4631 Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.050364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046761 restraints weight = 266918.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047689 restraints weight = 107840.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048226 restraints weight = 59907.851| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7330 Z= 0.193 Angle : 0.531 4.931 9950 Z= 0.279 Chirality : 0.035 0.107 1160 Planarity : 0.004 0.049 1250 Dihedral : 4.453 14.919 980 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.24 % Allowed : 8.80 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.30), residues: 860 helix: 1.32 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.92 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 11 HIS 0.001 0.000 HIS J 73 PHE 0.003 0.001 PHE G 17 TYR 0.005 0.001 TYR I 87 ARG 0.006 0.000 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.24 seconds wall clock time: 40 minutes 41.86 seconds (2441.86 seconds total)