Sun 23 Dec 22:23:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:19 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/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-1.8-parrot-hancs/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-hancs.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-hancs.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 3416 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Starting model: R = 0.3218 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2685 (Rfree = 0.000) for 3416 atoms. Found 158 (158 requested) and removed 82 (79 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.57 1.85 NCS extension: 0 residues added, 3492 seeds are put forward Round 1: 334 peptides, 17 chains. Longest chain 55 peptides. Score 0.922 Round 2: 352 peptides, 16 chains. Longest chain 46 peptides. Score 0.936 Round 3: 359 peptides, 8 chains. Longest chain 94 peptides. Score 0.964 Round 4: 365 peptides, 9 chains. Longest chain 73 peptides. Score 0.963 Round 5: 367 peptides, 8 chains. Longest chain 95 peptides. Score 0.967 Taking the results from Round 5 Chains 10, Residues 359, Estimated correctness of the model 99.9 % 6 chains (338 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 D and 79 D 8 chains (363 residues) following loop building 5 chains (343 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3574 restraints for refining 3339 atoms. 712 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2775 (Rfree = 0.000) for 3339 atoms. Found 115 (154 requested) and removed 67 (77 requested) atoms. Cycle 2: After refmac, R = 0.2539 (Rfree = 0.000) for 3382 atoms. Found 93 (153 requested) and removed 25 (78 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 3448 atoms. Found 90 (156 requested) and removed 8 (79 requested) atoms. Cycle 4: After refmac, R = 0.2184 (Rfree = 0.000) for 3525 atoms. Found 86 (160 requested) and removed 13 (81 requested) atoms. Cycle 5: After refmac, R = 0.2046 (Rfree = 0.000) for 3588 atoms. Found 80 (163 requested) and removed 14 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.55 1.82 NCS extension: 22 residues added (115 deleted due to clashes), 3678 seeds are put forward Round 1: 369 peptides, 7 chains. Longest chain 94 peptides. Score 0.970 Round 2: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 3: 372 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 4: 373 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 5: 372 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Taking the results from Round 5 Chains 6, Residues 367, Estimated correctness of the model 99.9 % 5 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 78 A 5 chains (370 residues) following loop building 4 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3525 restraints for refining 3508 atoms. 538 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2068 (Rfree = 0.000) for 3508 atoms. Found 136 (159 requested) and removed 39 (81 requested) atoms. Cycle 7: After refmac, R = 0.1954 (Rfree = 0.000) for 3598 atoms. Found 87 (163 requested) and removed 16 (83 requested) atoms. Cycle 8: After refmac, R = 0.1851 (Rfree = 0.000) for 3665 atoms. Found 83 (166 requested) and removed 25 (84 requested) atoms. Cycle 9: After refmac, R = 0.1794 (Rfree = 0.000) for 3719 atoms. Found 92 (169 requested) and removed 24 (86 requested) atoms. Cycle 10: After refmac, R = 0.1748 (Rfree = 0.000) for 3780 atoms. Found 69 (171 requested) and removed 36 (87 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3813 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 96 peptides. Score 0.979 Round 2: 374 peptides, 6 chains. Longest chain 93 peptides. Score 0.974 Round 3: 374 peptides, 4 chains. Longest chain 96 peptides. Score 0.979 Round 4: 373 peptides, 6 chains. Longest chain 93 peptides. Score 0.974 Round 5: 374 peptides, 4 chains. Longest chain 96 peptides. Score 0.979 Taking the results from Round 5 Chains 5, Residues 370, Estimated correctness of the model 100.0 % 4 chains (369 residues) have been docked in sequence Building loops using Loopy2018 5 chains (370 residues) following loop building 5 chains (370 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3576 restraints for refining 3606 atoms. 585 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1896 (Rfree = 0.000) for 3606 atoms. Found 146 (159 requested) and removed 30 (83 requested) atoms. Cycle 12: After refmac, R = 0.1795 (Rfree = 0.000) for 3717 atoms. Found 91 (165 requested) and removed 23 (86 requested) atoms. Cycle 13: After refmac, R = 0.1723 (Rfree = 0.000) for 3780 atoms. Found 74 (168 requested) and removed 26 (87 requested) atoms. Cycle 14: After refmac, R = 0.1676 (Rfree = 0.000) for 3824 atoms. Found 88 (170 requested) and removed 27 (88 requested) atoms. Cycle 15: After refmac, R = 0.1659 (Rfree = 0.000) for 3877 atoms. Found 87 (172 requested) and removed 34 (89 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.54 1.81 NCS extension: 0 residues added, 3930 seeds are put forward Round 1: 373 peptides, 4 chains. Longest chain 95 peptides. Score 0.979 Round 2: 371 peptides, 7 chains. Longest chain 93 peptides. Score 0.971 Round 3: 373 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 4: 371 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 5: 373 peptides, 4 chains. Longest chain 95 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 3625 restraints for refining 3679 atoms. 640 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1849 (Rfree = 0.000) for 3679 atoms. Found 153 (163 requested) and removed 35 (85 requested) atoms. Cycle 17: After refmac, R = 0.1749 (Rfree = 0.000) for 3792 atoms. Found 82 (168 requested) and removed 27 (87 requested) atoms. Cycle 18: After refmac, R = 0.1669 (Rfree = 0.000) for 3841 atoms. Found 72 (170 requested) and removed 31 (88 requested) atoms. Cycle 19: After refmac, R = 0.1621 (Rfree = 0.000) for 3880 atoms. Found 79 (172 requested) and removed 27 (89 requested) atoms. Cycle 20: After refmac, R = 0.1589 (Rfree = 0.000) for 3927 atoms. Found 89 (174 requested) and removed 35 (90 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 3981 seeds are put forward Round 1: 373 peptides, 5 chains. Longest chain 95 peptides. Score 0.976 Round 2: 372 peptides, 6 chains. Longest chain 95 peptides. Score 0.973 Round 3: 369 peptides, 8 chains. Longest chain 91 peptides. Score 0.967 Round 4: 375 peptides, 4 chains. Longest chain 95 peptides. Score 0.979 Round 5: 371 peptides, 7 chains. Longest chain 95 peptides. Score 0.971 Taking the results from Round 4 Chains 4, Residues 371, Estimated correctness of the model 100.0 % 4 chains (371 residues) have been docked in sequence Building loops using Loopy2018 4 chains (371 residues) following loop building 4 chains (371 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3670 restraints for refining 3731 atoms. 666 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1808 (Rfree = 0.000) for 3731 atoms. Found 158 (165 requested) and removed 30 (86 requested) atoms. Cycle 22: After refmac, R = 0.1723 (Rfree = 0.000) for 3853 atoms. Found 89 (171 requested) and removed 38 (89 requested) atoms. Cycle 23: After refmac, R = 0.1657 (Rfree = 0.000) for 3901 atoms. Found 94 (173 requested) and removed 25 (90 requested) atoms. Cycle 24: After refmac, R = 0.1617 (Rfree = 0.000) for 3968 atoms. Found 74 (176 requested) and removed 44 (91 requested) atoms. Cycle 25: After refmac, R = 0.1583 (Rfree = 0.000) for 3992 atoms. Found 88 (173 requested) and removed 46 (92 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.54 1.81 NCS extension: 0 residues added, 4034 seeds are put forward Round 1: 371 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 2: 371 peptides, 6 chains. Longest chain 95 peptides. Score 0.973 Round 3: 370 peptides, 6 chains. Longest chain 95 peptides. Score 0.973 Round 4: 371 peptides, 6 chains. Longest chain 95 peptides. Score 0.973 Round 5: 369 peptides, 8 chains. Longest chain 91 peptides. Score 0.967 Taking the results from Round 1 Chains 6, Residues 366, Estimated correctness of the model 99.9 % 5 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A 5 chains (368 residues) following loop building 5 chains (368 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3861 restraints for refining 3789 atoms. 887 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1786 (Rfree = 0.000) for 3789 atoms. Found 154 (161 requested) and removed 23 (87 requested) atoms. Cycle 27: After refmac, R = 0.1697 (Rfree = 0.000) for 3915 atoms. Found 92 (167 requested) and removed 34 (90 requested) atoms. Cycle 28: After refmac, R = 0.1641 (Rfree = 0.000) for 3969 atoms. Found 106 (168 requested) and removed 36 (91 requested) atoms. Cycle 29: After refmac, R = 0.1597 (Rfree = 0.000) for 4033 atoms. Found 81 (171 requested) and removed 45 (93 requested) atoms. Cycle 30: After refmac, R = 0.1566 (Rfree = 0.000) for 4066 atoms. Found 81 (169 requested) and removed 51 (94 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.56 1.84 NCS extension: 1 residues added (2 deleted due to clashes), 4097 seeds are put forward Round 1: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 2: 370 peptides, 7 chains. Longest chain 94 peptides. Score 0.970 Round 3: 370 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 4: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 5: 372 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Taking the results from Round 5 Chains 7, Residues 366, Estimated correctness of the model 99.9 % 5 chains (354 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 D and 60 D 6 chains (368 residues) following loop building 4 chains (356 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 4060 restraints for refining 3811 atoms. 1136 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1826 (Rfree = 0.000) for 3811 atoms. Found 155 (155 requested) and removed 30 (88 requested) atoms. Cycle 32: After refmac, R = 0.1728 (Rfree = 0.000) for 3929 atoms. Found 112 (160 requested) and removed 36 (91 requested) atoms. Cycle 33: After refmac, R = 0.1642 (Rfree = 0.000) for 3999 atoms. Found 95 (163 requested) and removed 35 (92 requested) atoms. Cycle 34: After refmac, R = 0.1606 (Rfree = 0.000) for 4056 atoms. Found 92 (165 requested) and removed 57 (93 requested) atoms. Cycle 35: After refmac, R = 0.1583 (Rfree = 0.000) for 4085 atoms. Found 101 (163 requested) and removed 47 (94 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added (27 deleted due to clashes), 4139 seeds are put forward Round 1: 374 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 2: 373 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 3: 373 peptides, 6 chains. Longest chain 94 peptides. Score 0.974 Round 4: 371 peptides, 7 chains. Longest chain 94 peptides. Score 0.971 Round 5: 371 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Taking the results from Round 1 Chains 6, Residues 369, Estimated correctness of the model 99.9 % 5 chains (368 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 D and 60 D 5 chains (371 residues) following loop building 5 chains (371 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3930 restraints for refining 3852 atoms. 927 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1779 (Rfree = 0.000) for 3852 atoms. Found 153 (153 requested) and removed 26 (89 requested) atoms. Cycle 37: After refmac, R = 0.1672 (Rfree = 0.000) for 3974 atoms. Found 109 (158 requested) and removed 40 (92 requested) atoms. Cycle 38: After refmac, R = 0.1602 (Rfree = 0.000) for 4039 atoms. Found 102 (161 requested) and removed 36 (93 requested) atoms. Cycle 39: After refmac, R = 0.1563 (Rfree = 0.000) for 4094 atoms. Found 104 (163 requested) and removed 44 (94 requested) atoms. Cycle 40: After refmac, R = 0.1536 (Rfree = 0.000) for 4152 atoms. Found 92 (165 requested) and removed 54 (96 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.54 1.81 NCS extension: 0 residues added, 4190 seeds are put forward Round 1: 372 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 2: 369 peptides, 7 chains. Longest chain 94 peptides. Score 0.970 Round 3: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 4: 371 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 5: 372 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Taking the results from Round 1 Chains 5, Residues 367, Estimated correctness of the model 99.9 % 5 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 D and 60 D 4 chains (369 residues) following loop building 4 chains (369 residues) in sequence following loop building ------------------------------------------------------ 27534 reflections ( 89.33 % complete ) and 3952 restraints for refining 3877 atoms. 967 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1766 (Rfree = 0.000) for 3877 atoms. Found 150 (150 requested) and removed 28 (89 requested) atoms. Cycle 42: After refmac, R = 0.1683 (Rfree = 0.000) for 3992 atoms. Found 92 (155 requested) and removed 24 (92 requested) atoms. Cycle 43: After refmac, R = 0.1600 (Rfree = 0.000) for 4058 atoms. Found 83 (157 requested) and removed 34 (93 requested) atoms. Cycle 44: After refmac, R = 0.1566 (Rfree = 0.000) for 4102 atoms. Found 91 (159 requested) and removed 42 (94 requested) atoms. Cycle 45: After refmac, R = 0.1539 (Rfree = 0.000) for 4147 atoms. Found 83 (161 requested) and removed 48 (96 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.55 1.82 NCS extension: 0 residues added, 4182 seeds are put forward Round 1: 372 peptides, 5 chains. Longest chain 94 peptides. Score 0.976 Round 2: 370 peptides, 7 chains. Longest chain 95 peptides. Score 0.970 Round 3: 370 peptides, 6 chains. Longest chain 93 peptides. Score 0.973 Round 4: 371 peptides, 6 chains. Longest chain 94 peptides. Score 0.973 Round 5: 368 peptides, 7 chains. Longest chain 93 peptides. Score 0.970 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 367, Estimated correctness of the model 99.9 % 5 chains (367 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 57 D and 60 D 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 2985 restraints for refining 2905 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2585 (Rfree = 0.000) for 2905 atoms. Found 78 (110 requested) and removed 0 (110 requested) atoms. Cycle 47: After refmac, R = 0.2339 (Rfree = 0.000) for 2905 atoms. Found 38 (112 requested) and removed 2 (68 requested) atoms. Cycle 48: After refmac, R = 0.2202 (Rfree = 0.000) for 2905 atoms. Found 13 (114 requested) and removed 3 (69 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 2905 atoms. TimeTaking 62.95