Mon 24 Dec 01:07:48 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-mrncs ############### 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 01:07:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-mrncs/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-mrncs.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-mrncs.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 3445 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2647 (Rfree = 0.000) for 3445 atoms. Found 159 (159 requested) and removed 83 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3521 seeds are put forward Round 1: 350 peptides, 13 chains. Longest chain 67 peptides. Score 0.946 Round 2: 364 peptides, 10 chains. Longest chain 92 peptides. Score 0.960 Round 3: 370 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 4: 369 peptides, 7 chains. Longest chain 92 peptides. Score 0.970 Round 5: 366 peptides, 10 chains. Longest chain 95 peptides. Score 0.961 Taking the results from Round 3 Chains 5, Residues 365, Estimated correctness of the model 99.9 % 5 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 C and 59 C 4 chains (369 residues) following loop building 4 chains (369 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3341 restraints for refining 3354 atoms. 353 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2712 (Rfree = 0.000) for 3354 atoms. Found 119 (155 requested) and removed 58 (77 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 3411 atoms. Found 80 (157 requested) and removed 15 (78 requested) atoms. Cycle 3: After refmac, R = 0.2284 (Rfree = 0.000) for 3468 atoms. Found 68 (160 requested) and removed 12 (80 requested) atoms. Cycle 4: After refmac, R = 0.2071 (Rfree = 0.000) for 3521 atoms. Found 82 (163 requested) and removed 12 (81 requested) atoms. Cycle 5: After refmac, R = 0.1979 (Rfree = 0.000) for 3580 atoms. Found 61 (166 requested) and removed 10 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.54 1.81 NCS extension: 0 residues added, 3634 seeds are put forward Round 1: 371 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 2: 372 peptides, 7 chains. Longest chain 94 peptides. Score 0.971 Round 3: 371 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 4: 372 peptides, 7 chains. Longest chain 94 peptides. Score 0.971 Round 5: 371 peptides, 6 chains. Longest chain 95 peptides. Score 0.973 Taking the results from Round 3 Chains 5, Residues 366, Estimated correctness of the model 99.9 % 5 chains (366 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 C and 49 C 4 chains (368 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3488 restraints for refining 3484 atoms. 511 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2040 (Rfree = 0.000) for 3484 atoms. Found 145 (161 requested) and removed 31 (80 requested) atoms. Cycle 7: After refmac, R = 0.1911 (Rfree = 0.000) for 3595 atoms. Found 94 (166 requested) and removed 17 (83 requested) atoms. Cycle 8: After refmac, R = 0.1845 (Rfree = 0.000) for 3664 atoms. Found 85 (169 requested) and removed 19 (84 requested) atoms. Cycle 9: After refmac, R = 0.1781 (Rfree = 0.000) for 3723 atoms. Found 72 (172 requested) and removed 21 (86 requested) atoms. Cycle 10: After refmac, R = 0.1720 (Rfree = 0.000) for 3771 atoms. Found 65 (174 requested) and removed 23 (87 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.56 1.84 NCS extension: 0 residues added, 3813 seeds are put forward Round 1: 375 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 2: 375 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 374 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 4: 372 peptides, 7 chains. Longest chain 95 peptides. Score 0.971 Round 5: 375 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Taking the results from Round 2 Chains 6, Residues 370, Estimated correctness of the model 99.9 % 5 chains (369 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 59 A 5 chains (372 residues) following loop building 5 chains (372 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3568 restraints for refining 3613 atoms. 560 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1918 (Rfree = 0.000) for 3613 atoms. Found 135 (167 requested) and removed 28 (83 requested) atoms. Cycle 12: After refmac, R = 0.1811 (Rfree = 0.000) for 3712 atoms. Found 104 (172 requested) and removed 19 (86 requested) atoms. Cycle 13: After refmac, R = 0.1751 (Rfree = 0.000) for 3796 atoms. Found 89 (175 requested) and removed 30 (87 requested) atoms. Cycle 14: After refmac, R = 0.1698 (Rfree = 0.000) for 3852 atoms. Found 79 (178 requested) and removed 35 (89 requested) atoms. Cycle 15: After refmac, R = 0.1651 (Rfree = 0.000) for 3891 atoms. Found 79 (180 requested) and removed 34 (90 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3936 seeds are put forward Round 1: 375 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 2: 375 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 372 peptides, 8 chains. Longest chain 92 peptides. Score 0.968 Round 4: 375 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 5: 372 peptides, 8 chains. Longest chain 92 peptides. Score 0.968 Taking the results from Round 4 Chains 5, Residues 370, Estimated correctness of the model 99.9 % 5 chains (370 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 59 B 4 chains (372 residues) following loop building 4 chains (372 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3622 restraints for refining 3670 atoms. 612 conditional restraints added. Observations/parameters ratio is 1.88 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1855 (Rfree = 0.000) for 3670 atoms. Found 151 (169 requested) and removed 27 (84 requested) atoms. Cycle 17: After refmac, R = 0.1753 (Rfree = 0.000) for 3786 atoms. Found 81 (175 requested) and removed 14 (87 requested) atoms. Cycle 18: After refmac, R = 0.1671 (Rfree = 0.000) for 3847 atoms. Found 71 (178 requested) and removed 21 (89 requested) atoms. Cycle 19: After refmac, R = 0.1627 (Rfree = 0.000) for 3890 atoms. Found 74 (180 requested) and removed 23 (90 requested) atoms. Cycle 20: After refmac, R = 0.1614 (Rfree = 0.000) for 3936 atoms. Found 82 (182 requested) and removed 40 (91 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.56 1.84 NCS extension: 0 residues added, 3978 seeds are put forward Round 1: 375 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 2: 374 peptides, 4 chains. Longest chain 95 peptides. Score 0.979 Round 3: 371 peptides, 7 chains. Longest chain 95 peptides. Score 0.971 Round 4: 372 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 5: 374 peptides, 4 chains. Longest chain 95 peptides. Score 0.979 Taking the results from Round 5 Chains 4, Residues 370, Estimated correctness of the model 100.0 % 4 chains (370 residues) have been docked in sequence Building loops using Loopy2018 4 chains (370 residues) following loop building 4 chains (370 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3691 restraints for refining 3699 atoms. 697 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1840 (Rfree = 0.000) for 3699 atoms. Found 171 (171 requested) and removed 23 (85 requested) atoms. Cycle 22: After refmac, R = 0.1749 (Rfree = 0.000) for 3840 atoms. Found 99 (177 requested) and removed 18 (88 requested) atoms. Cycle 23: After refmac, R = 0.1674 (Rfree = 0.000) for 3915 atoms. Found 88 (181 requested) and removed 31 (90 requested) atoms. Cycle 24: After refmac, R = 0.1627 (Rfree = 0.000) for 3969 atoms. Found 73 (183 requested) and removed 40 (91 requested) atoms. Cycle 25: After refmac, R = 0.1582 (Rfree = 0.000) for 3995 atoms. Found 86 (181 requested) and removed 39 (92 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4042 seeds are put forward Round 1: 373 peptides, 7 chains. Longest chain 94 peptides. Score 0.971 Round 2: 376 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 374 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 4: 372 peptides, 7 chains. Longest chain 96 peptides. Score 0.971 Round 5: 373 peptides, 5 chains. Longest chain 96 peptides. Score 0.976 Taking the results from Round 2 Chains 6, Residues 371, Estimated correctness of the model 99.9 % 5 chains (370 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 59 B 5 chains (373 residues) following loop building 5 chains (373 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3721 restraints for refining 3762 atoms. 702 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1799 (Rfree = 0.000) for 3762 atoms. Found 160 (171 requested) and removed 27 (87 requested) atoms. Cycle 27: After refmac, R = 0.1724 (Rfree = 0.000) for 3884 atoms. Found 105 (176 requested) and removed 33 (90 requested) atoms. Cycle 28: After refmac, R = 0.1667 (Rfree = 0.000) for 3949 atoms. Found 94 (178 requested) and removed 36 (91 requested) atoms. Cycle 29: After refmac, R = 0.1624 (Rfree = 0.000) for 4002 atoms. Found 95 (181 requested) and removed 44 (92 requested) atoms. Cycle 30: After refmac, R = 0.1625 (Rfree = 0.000) for 4046 atoms. Found 96 (183 requested) and removed 57 (93 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.56 1.84 NCS extension: 0 residues added, 4085 seeds are put forward Round 1: 374 peptides, 6 chains. Longest chain 95 peptides. Score 0.974 Round 2: 376 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 372 peptides, 8 chains. Longest chain 92 peptides. Score 0.968 Round 4: 375 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 5: 374 peptides, 7 chains. Longest chain 96 peptides. Score 0.971 Taking the results from Round 4 Chains 6, Residues 370, Estimated correctness of the model 99.9 % 5 chains (369 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 B and 45 B 5 chains (372 residues) following loop building 5 chains (372 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3788 restraints for refining 3809 atoms. 778 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1825 (Rfree = 0.000) for 3809 atoms. Found 169 (169 requested) and removed 26 (88 requested) atoms. Cycle 32: After refmac, R = 0.1728 (Rfree = 0.000) for 3945 atoms. Found 112 (175 requested) and removed 34 (91 requested) atoms. Cycle 33: After refmac, R = 0.1670 (Rfree = 0.000) for 4013 atoms. Found 94 (179 requested) and removed 37 (93 requested) atoms. Cycle 34: After refmac, R = 0.1626 (Rfree = 0.000) for 4066 atoms. Found 85 (180 requested) and removed 33 (94 requested) atoms. Cycle 35: After refmac, R = 0.1586 (Rfree = 0.000) for 4111 atoms. Found 97 (182 requested) and removed 52 (95 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4156 seeds are put forward Round 1: 375 peptides, 6 chains. Longest chain 95 peptides. Score 0.974 Round 2: 378 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 375 peptides, 6 chains. Longest chain 96 peptides. Score 0.974 Round 4: 379 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 5: 377 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Taking the results from Round 5 Chains 6, Residues 372, Estimated correctness of the model 99.9 % 5 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 D and 46 D 5 chains (374 residues) following loop building 5 chains (374 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3820 restraints for refining 3854 atoms. 792 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1848 (Rfree = 0.000) for 3854 atoms. Found 167 (167 requested) and removed 32 (89 requested) atoms. Cycle 37: After refmac, R = 0.1758 (Rfree = 0.000) for 3981 atoms. Found 108 (173 requested) and removed 33 (92 requested) atoms. Cycle 38: After refmac, R = 0.1679 (Rfree = 0.000) for 4046 atoms. Found 97 (176 requested) and removed 32 (93 requested) atoms. Cycle 39: After refmac, R = 0.1633 (Rfree = 0.000) for 4099 atoms. Found 87 (179 requested) and removed 44 (95 requested) atoms. Cycle 40: After refmac, R = 0.1602 (Rfree = 0.000) for 4136 atoms. Found 94 (176 requested) and removed 40 (95 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4190 seeds are put forward Round 1: 376 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 2: 376 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 3: 376 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 4: 373 peptides, 7 chains. Longest chain 96 peptides. Score 0.971 Round 5: 374 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Taking the results from Round 3 Chains 5, Residues 371, Estimated correctness of the model 99.9 % 5 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A 4 chains (373 residues) following loop building 4 chains (373 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3925 restraints for refining 3884 atoms. 904 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1821 (Rfree = 0.000) for 3884 atoms. Found 165 (165 requested) and removed 26 (89 requested) atoms. Cycle 42: After refmac, R = 0.1740 (Rfree = 0.000) for 4014 atoms. Found 126 (171 requested) and removed 30 (93 requested) atoms. Cycle 43: After refmac, R = 0.1659 (Rfree = 0.000) for 4103 atoms. Found 95 (175 requested) and removed 44 (95 requested) atoms. Cycle 44: After refmac, R = 0.1607 (Rfree = 0.000) for 4150 atoms. Found 104 (177 requested) and removed 44 (96 requested) atoms. Cycle 45: After refmac, R = 0.1577 (Rfree = 0.000) for 4206 atoms. Found 95 (178 requested) and removed 48 (97 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4253 seeds are put forward Round 1: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 2: 377 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 3: 372 peptides, 8 chains. Longest chain 92 peptides. Score 0.968 Round 4: 375 peptides, 5 chains. Longest chain 96 peptides. Score 0.977 Round 5: 373 peptides, 8 chains. Longest chain 92 peptides. Score 0.968 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 370, Estimated correctness of the model 99.9 % 5 chains (370 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 56 D and 59 D 4 chains (372 residues) following loop building 4 chains (372 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 27534 reflections ( 89.33 % complete ) and 3013 restraints for refining 2933 atoms. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2561 (Rfree = 0.000) for 2933 atoms. Found 67 (121 requested) and removed 0 (121 requested) atoms. Cycle 47: After refmac, R = 0.2320 (Rfree = 0.000) for 2933 atoms. Found 25 (124 requested) and removed 2 (69 requested) atoms. Cycle 48: After refmac, R = 0.2232 (Rfree = 0.000) for 2933 atoms. Found 22 (125 requested) and removed 4 (69 requested) atoms. Cycle 49: After refmac, R = 0.2179 (Rfree = 0.000) for 2933 atoms. Found 9 (126 requested) and removed 1 (70 requested) atoms. Writing output files ... TimeTaking 55.95