Mon 24 Dec 07:34:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:35:00 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.4198 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-1.8-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-1.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.45 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 50.895 1.800 Wilson plot Bfac: 10.34 27534 reflections ( 89.33 % complete ) and 0 restraints for refining 3431 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Starting model: R = 0.3291 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2795 (Rfree = 0.000) for 3431 atoms. Found 150 (158 requested) and removed 87 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3494 seeds are put forward Round 1: 266 peptides, 30 chains. Longest chain 43 peptides. Score 0.744 Round 2: 313 peptides, 20 chains. Longest chain 63 peptides. Score 0.892 Round 3: 339 peptides, 15 chains. Longest chain 55 peptides. Score 0.933 Round 4: 348 peptides, 14 chains. Longest chain 76 peptides. Score 0.941 Round 5: 352 peptides, 10 chains. Longest chain 93 peptides. Score 0.956 Taking the results from Round 5 Chains 14, Residues 342, Estimated correctness of the model 99.8 % 8 chains (302 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 C and 31 C Built loop between residues 26 D and 30 D Built loop between residues 46 D and 49 D 10 chains (348 residues) following loop building 5 chains (311 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3803 restraints for refining 3348 atoms. 1152 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2981 (Rfree = 0.000) for 3348 atoms. Found 137 (154 requested) and removed 80 (77 requested) atoms. Cycle 2: After refmac, R = 0.2721 (Rfree = 0.000) for 3395 atoms. Found 98 (154 requested) and removed 46 (78 requested) atoms. Cycle 3: After refmac, R = 0.2559 (Rfree = 0.000) for 3445 atoms. Found 87 (156 requested) and removed 12 (79 requested) atoms. Cycle 4: After refmac, R = 0.2345 (Rfree = 0.000) for 3515 atoms. Found 89 (159 requested) and removed 10 (81 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 3590 atoms. Found 91 (163 requested) and removed 16 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.54 1.81 NCS extension: 32 residues added (111 deleted due to clashes), 3701 seeds are put forward Round 1: 360 peptides, 6 chains. Longest chain 91 peptides. Score 0.970 Round 2: 362 peptides, 5 chains. Longest chain 94 peptides. Score 0.974 Round 3: 362 peptides, 8 chains. Longest chain 91 peptides. Score 0.965 Round 4: 364 peptides, 5 chains. Longest chain 94 peptides. Score 0.974 Round 5: 360 peptides, 10 chains. Longest chain 91 peptides. Score 0.959 Taking the results from Round 4 Chains 5, Residues 359, Estimated correctness of the model 99.9 % 5 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 C and 59 C 4 chains (364 residues) following loop building 4 chains (364 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3596 restraints for refining 3556 atoms. 649 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2348 (Rfree = 0.000) for 3556 atoms. Found 137 (161 requested) and removed 53 (82 requested) atoms. Cycle 7: After refmac, R = 0.2164 (Rfree = 0.000) for 3635 atoms. Found 95 (165 requested) and removed 17 (84 requested) atoms. Cycle 8: After refmac, R = 0.2045 (Rfree = 0.000) for 3704 atoms. Found 73 (168 requested) and removed 10 (85 requested) atoms. Cycle 9: After refmac, R = 0.1963 (Rfree = 0.000) for 3755 atoms. Found 72 (171 requested) and removed 15 (87 requested) atoms. Cycle 10: After refmac, R = 0.1901 (Rfree = 0.000) for 3804 atoms. Found 67 (172 requested) and removed 18 (88 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.54 1.81 NCS extension: 0 residues added, 3853 seeds are put forward Round 1: 368 peptides, 6 chains. Longest chain 94 peptides. Score 0.972 Round 2: 367 peptides, 7 chains. Longest chain 91 peptides. Score 0.970 Round 3: 366 peptides, 7 chains. Longest chain 94 peptides. Score 0.969 Round 4: 371 peptides, 7 chains. Longest chain 93 peptides. Score 0.971 Round 5: 369 peptides, 8 chains. Longest chain 94 peptides. Score 0.967 Taking the results from Round 1 Chains 7, Residues 362, Estimated correctness of the model 99.9 % 6 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 59 A Built loop between residues 56 D and 59 D 4 chains (366 residues) following loop building 4 chains (366 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3702 restraints for refining 3691 atoms. 736 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2034 (Rfree = 0.000) for 3691 atoms. Found 123 (167 requested) and removed 29 (85 requested) atoms. Cycle 12: After refmac, R = 0.1924 (Rfree = 0.000) for 3778 atoms. Found 77 (171 requested) and removed 22 (87 requested) atoms. Cycle 13: After refmac, R = 0.1859 (Rfree = 0.000) for 3825 atoms. Found 73 (173 requested) and removed 11 (88 requested) atoms. Cycle 14: After refmac, R = 0.1795 (Rfree = 0.000) for 3882 atoms. Found 73 (175 requested) and removed 27 (89 requested) atoms. Cycle 15: After refmac, R = 0.1745 (Rfree = 0.000) for 3919 atoms. Found 71 (177 requested) and removed 22 (90 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3968 seeds are put forward Round 1: 368 peptides, 5 chains. Longest chain 93 peptides. Score 0.975 Round 2: 369 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 3: 370 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 4: 364 peptides, 8 chains. Longest chain 92 peptides. Score 0.966 Round 5: 371 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Taking the results from Round 5 Chains 8, Residues 366, Estimated correctness of the model 99.9 % 6 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 C and 72 C 5 chains (369 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3773 restraints for refining 3741 atoms. 789 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2253 (Rfree = 0.000) for 3741 atoms. Found 110 (170 requested) and removed 56 (86 requested) atoms. Cycle 17: After refmac, R = 0.1978 (Rfree = 0.000) for 3789 atoms. Found 83 (168 requested) and removed 12 (87 requested) atoms. Cycle 18: After refmac, R = 0.1872 (Rfree = 0.000) for 3847 atoms. Found 71 (171 requested) and removed 16 (89 requested) atoms. Cycle 19: After refmac, R = 0.1794 (Rfree = 0.000) for 3898 atoms. Found 78 (173 requested) and removed 20 (90 requested) atoms. Cycle 20: After refmac, R = 0.1741 (Rfree = 0.000) for 3953 atoms. Found 71 (175 requested) and removed 27 (91 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.54 1.81 NCS extension: 8 residues added (89 deleted due to clashes), 4013 seeds are put forward Round 1: 368 peptides, 7 chains. Longest chain 94 peptides. Score 0.970 Round 2: 370 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 3: 368 peptides, 5 chains. Longest chain 94 peptides. Score 0.975 Round 4: 369 peptides, 7 chains. Longest chain 93 peptides. Score 0.970 Round 5: 372 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Taking the results from Round 5 Chains 4, Residues 368, Estimated correctness of the model 100.0 % 4 chains (368 residues) have been docked in sequence Building loops using Loopy2018 4 chains (368 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3760 restraints for refining 3754 atoms. 783 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1908 (Rfree = 0.000) for 3754 atoms. Found 145 (166 requested) and removed 36 (86 requested) atoms. Cycle 22: After refmac, R = 0.1816 (Rfree = 0.000) for 3853 atoms. Found 84 (171 requested) and removed 24 (89 requested) atoms. Cycle 23: After refmac, R = 0.1731 (Rfree = 0.000) for 3911 atoms. Found 81 (174 requested) and removed 20 (90 requested) atoms. Cycle 24: After refmac, R = 0.1689 (Rfree = 0.000) for 3964 atoms. Found 74 (176 requested) and removed 31 (91 requested) atoms. Cycle 25: After refmac, R = 0.1653 (Rfree = 0.000) for 4002 atoms. Found 78 (178 requested) and removed 35 (92 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4046 seeds are put forward Round 1: 369 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 2: 371 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 3: 370 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 4: 372 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Round 5: 370 peptides, 7 chains. Longest chain 93 peptides. Score 0.970 Taking the results from Round 4 Chains 4, Residues 368, Estimated correctness of the model 100.0 % 4 chains (368 residues) have been docked in sequence Building loops using Loopy2018 4 chains (368 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3772 restraints for refining 3779 atoms. 792 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1904 (Rfree = 0.000) for 3779 atoms. Found 137 (167 requested) and removed 34 (87 requested) atoms. Cycle 27: After refmac, R = 0.1780 (Rfree = 0.000) for 3871 atoms. Found 79 (172 requested) and removed 17 (89 requested) atoms. Cycle 28: After refmac, R = 0.1697 (Rfree = 0.000) for 3928 atoms. Found 73 (174 requested) and removed 17 (90 requested) atoms. Cycle 29: After refmac, R = 0.1653 (Rfree = 0.000) for 3976 atoms. Found 64 (177 requested) and removed 33 (92 requested) atoms. Cycle 30: After refmac, R = 0.1617 (Rfree = 0.000) for 4004 atoms. Found 81 (174 requested) and removed 30 (92 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4056 seeds are put forward Round 1: 368 peptides, 6 chains. Longest chain 93 peptides. Score 0.972 Round 2: 370 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 3: 370 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 4: 372 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Round 5: 369 peptides, 7 chains. Longest chain 93 peptides. Score 0.970 Taking the results from Round 4 Chains 4, Residues 368, Estimated correctness of the model 100.0 % 4 chains (368 residues) have been docked in sequence Building loops using Loopy2018 4 chains (368 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3855 restraints for refining 3801 atoms. 875 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1843 (Rfree = 0.000) for 3801 atoms. Found 158 (164 requested) and removed 28 (87 requested) atoms. Cycle 32: After refmac, R = 0.1733 (Rfree = 0.000) for 3921 atoms. Found 106 (170 requested) and removed 34 (90 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1685 (Rfree = 0.000) for 3986 atoms. Found 95 (173 requested) and removed 38 (92 requested) atoms. Cycle 34: After refmac, R = 0.1638 (Rfree = 0.000) for 4035 atoms. Found 78 (176 requested) and removed 31 (93 requested) atoms. Cycle 35: After refmac, R = 0.1604 (Rfree = 0.000) for 4072 atoms. Found 70 (177 requested) and removed 50 (94 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4093 seeds are put forward Round 1: 372 peptides, 5 chains. Longest chain 93 peptides. Score 0.976 Round 2: 373 peptides, 4 chains. Longest chain 95 peptides. Score 0.979 Round 3: 371 peptides, 7 chains. Longest chain 93 peptides. Score 0.971 Round 4: 372 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 5: 369 peptides, 7 chains. Longest chain 93 peptides. Score 0.970 Taking the results from Round 2 Chains 4, Residues 369, Estimated correctness of the model 100.0 % 4 chains (369 residues) have been docked in sequence Building loops using Loopy2018 4 chains (369 residues) following loop building 4 chains (369 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3874 restraints for refining 3847 atoms. 889 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1821 (Rfree = 0.000) for 3847 atoms. Found 163 (163 requested) and removed 28 (88 requested) atoms. Cycle 37: After refmac, R = 0.1723 (Rfree = 0.000) for 3973 atoms. Found 116 (169 requested) and removed 32 (92 requested) atoms. Cycle 38: After refmac, R = 0.1643 (Rfree = 0.000) for 4052 atoms. Found 85 (172 requested) and removed 43 (93 requested) atoms. Cycle 39: After refmac, R = 0.1604 (Rfree = 0.000) for 4085 atoms. Found 91 (170 requested) and removed 34 (94 requested) atoms. Cycle 40: After refmac, R = 0.1568 (Rfree = 0.000) for 4135 atoms. Found 81 (172 requested) and removed 54 (95 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4163 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Round 2: 372 peptides, 5 chains. Longest chain 93 peptides. Score 0.976 Round 3: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 4: 369 peptides, 8 chains. Longest chain 93 peptides. Score 0.967 Round 5: 373 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Taking the results from Round 5 Chains 4, Residues 369, Estimated correctness of the model 100.0 % 4 chains (369 residues) have been docked in sequence Building loops using Loopy2018 4 chains (369 residues) following loop building 4 chains (369 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3970 restraints for refining 3863 atoms. 983 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1820 (Rfree = 0.000) for 3863 atoms. Found 157 (157 requested) and removed 37 (89 requested) atoms. Cycle 42: After refmac, R = 0.1727 (Rfree = 0.000) for 3972 atoms. Found 108 (162 requested) and removed 25 (92 requested) atoms. Cycle 43: After refmac, R = 0.1653 (Rfree = 0.000) for 4052 atoms. Found 81 (165 requested) and removed 36 (93 requested) atoms. Cycle 44: After refmac, R = 0.1608 (Rfree = 0.000) for 4090 atoms. Found 91 (166 requested) and removed 40 (94 requested) atoms. Cycle 45: After refmac, R = 0.1578 (Rfree = 0.000) for 4135 atoms. Found 86 (168 requested) and removed 60 (95 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.53 1.80 NCS extension: 0 residues added, 4162 seeds are put forward Round 1: 371 peptides, 5 chains. Longest chain 93 peptides. Score 0.976 Round 2: 373 peptides, 4 chains. Longest chain 94 peptides. Score 0.979 Round 3: 372 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 4: 372 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 5: 371 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 369, Estimated correctness of the model 100.0 % 4 chains (369 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 4 chains (369 residues) following loop building 4 chains (369 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 27534 reflections ( 89.33 % complete ) and 2987 restraints for refining 2907 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2604 (Rfree = 0.000) for 2907 atoms. Found 71 (115 requested) and removed 0 (115 requested) atoms. Cycle 47: After refmac, R = 0.2358 (Rfree = 0.000) for 2907 atoms. Found 29 (118 requested) and removed 2 (68 requested) atoms. Cycle 48: After refmac, R = 0.2247 (Rfree = 0.000) for 2907 atoms. Found 21 (119 requested) and removed 4 (69 requested) atoms. Cycle 49: After refmac, R = 0.2183 (Rfree = 0.000) for 2907 atoms. TimeTaking 48.53