Tue 25 Dec 20:46:16 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 2a2m-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a2m-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a2m-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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/2a2m-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 ============================================================ Tue 25 Dec 20:46:35 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/2a2m-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 850 and 0 Target number of residues in the AU: 850 Target solvent content: 0.5144 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-1.9-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 0.75 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: 163.559 1.880 Wilson plot Bfac: 26.58 74702 reflections ( 94.58 % complete ) and 0 restraints for refining 4546 atoms. Observations/parameters ratio is 4.11 ------------------------------------------------------ Starting model: R = 0.3259 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2769 (Rfree = 0.000) for 4546 atoms. Found 185 (185 requested) and removed 72 (92 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.11 1.57 NCS extension: 0 residues added, 4659 seeds are put forward Round 1: 394 peptides, 31 chains. Longest chain 35 peptides. Score 0.645 Round 2: 416 peptides, 23 chains. Longest chain 42 peptides. Score 0.714 Round 3: 436 peptides, 10 chains. Longest chain 80 peptides. Score 0.795 Round 4: 441 peptides, 14 chains. Longest chain 86 peptides. Score 0.781 Round 5: 449 peptides, 7 chains. Longest chain 115 peptides. Score 0.818 Taking the results from Round 5 Chains 8, Residues 442, Estimated correctness of the model 97.4 % 7 chains (440 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 53 A Built loop between residues 95 A and 97 A Built loop between residues 203 A and 207 A Built loop between residues 96 B and 100 B Built loop between residues 132 B and 135 B 2 chains (453 residues) following loop building 2 chains (453 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4246 restraints for refining 4405 atoms. 504 conditional restraints added. Observations/parameters ratio is 4.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2596 (Rfree = 0.000) for 4405 atoms. Found 180 (180 requested) and removed 45 (90 requested) atoms. Cycle 2: After refmac, R = 0.2173 (Rfree = 0.000) for 4522 atoms. Found 185 (185 requested) and removed 33 (92 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1994 (Rfree = 0.000) for 4630 atoms. Found 191 (191 requested) and removed 38 (95 requested) atoms. Cycle 4: After refmac, R = 0.1930 (Rfree = 0.000) for 4749 atoms. Found 195 (195 requested) and removed 56 (97 requested) atoms. Cycle 5: After refmac, R = 0.1881 (Rfree = 0.000) for 4856 atoms. Found 172 (199 requested) and removed 71 (99 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.04 1.51 NCS extension: 0 residues added, 4958 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 227 peptides. Score 0.836 Round 2: 449 peptides, 5 chains. Longest chain 227 peptides. Score 0.826 Round 3: 450 peptides, 6 chains. Longest chain 116 peptides. Score 0.823 Round 4: 445 peptides, 8 chains. Longest chain 139 peptides. Score 0.811 Round 5: 451 peptides, 5 chains. Longest chain 116 peptides. Score 0.828 Taking the results from Round 1 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4325 restraints for refining 4493 atoms. 606 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1916 (Rfree = 0.000) for 4493 atoms. Found 183 (183 requested) and removed 34 (91 requested) atoms. Cycle 7: After refmac, R = 0.1835 (Rfree = 0.000) for 4619 atoms. Found 189 (189 requested) and removed 49 (94 requested) atoms. Cycle 8: After refmac, R = 0.1786 (Rfree = 0.000) for 4743 atoms. Found 180 (194 requested) and removed 58 (97 requested) atoms. Cycle 9: After refmac, R = 0.1764 (Rfree = 0.000) for 4851 atoms. Found 172 (198 requested) and removed 79 (99 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1760 (Rfree = 0.000) for 4922 atoms. Found 193 (202 requested) and removed 96 (101 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 5019 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 227 peptides. Score 0.836 Round 2: 449 peptides, 5 chains. Longest chain 152 peptides. Score 0.826 Round 3: 443 peptides, 10 chains. Longest chain 91 peptides. Score 0.801 Round 4: 452 peptides, 6 chains. Longest chain 118 peptides. Score 0.824 Round 5: 451 peptides, 7 chains. Longest chain 100 peptides. Score 0.819 Taking the results from Round 1 Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4399 restraints for refining 4547 atoms. 680 conditional restraints added. Observations/parameters ratio is 4.11 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1958 (Rfree = 0.000) for 4547 atoms. Found 185 (185 requested) and removed 16 (92 requested) atoms. Cycle 12: After refmac, R = 0.1821 (Rfree = 0.000) for 4699 atoms. Found 183 (192 requested) and removed 56 (96 requested) atoms. Cycle 13: After refmac, R = 0.1760 (Rfree = 0.000) for 4804 atoms. Found 195 (197 requested) and removed 79 (98 requested) atoms. Cycle 14: After refmac, R = 0.1739 (Rfree = 0.000) for 4893 atoms. Found 186 (201 requested) and removed 98 (100 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1710 (Rfree = 0.000) for 4955 atoms. Found 197 (199 requested) and removed 110 (101 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 5042 seeds are put forward Round 1: 449 peptides, 3 chains. Longest chain 226 peptides. Score 0.834 Round 2: 443 peptides, 6 chains. Longest chain 152 peptides. Score 0.818 Round 3: 449 peptides, 4 chains. Longest chain 201 peptides. Score 0.830 Round 4: 450 peptides, 7 chains. Longest chain 169 peptides. Score 0.819 Round 5: 448 peptides, 9 chains. Longest chain 96 peptides. Score 0.809 Taking the results from Round 1 Chains 3, Residues 446, Estimated correctness of the model 97.8 % 3 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 190 B and 193 B 2 chains (448 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4391 restraints for refining 4554 atoms. 685 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1959 (Rfree = 0.000) for 4554 atoms. Found 179 (179 requested) and removed 19 (93 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1826 (Rfree = 0.000) for 4705 atoms. Found 172 (184 requested) and removed 49 (96 requested) atoms. Cycle 18: After refmac, R = 0.1771 (Rfree = 0.000) for 4807 atoms. Found 136 (189 requested) and removed 72 (98 requested) atoms. Cycle 19: After refmac, R = 0.1729 (Rfree = 0.000) for 4852 atoms. Found 181 (187 requested) and removed 63 (99 requested) atoms. Cycle 20: After refmac, R = 0.1722 (Rfree = 0.000) for 4947 atoms. Found 167 (191 requested) and removed 104 (101 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.03 1.51 NCS extension: 0 residues added, 5011 seeds are put forward Round 1: 452 peptides, 4 chains. Longest chain 226 peptides. Score 0.832 Round 2: 450 peptides, 5 chains. Longest chain 226 peptides. Score 0.827 Round 3: 451 peptides, 7 chains. Longest chain 138 peptides. Score 0.819 Round 4: 449 peptides, 6 chains. Longest chain 150 peptides. Score 0.822 Round 5: 450 peptides, 5 chains. Longest chain 226 peptides. Score 0.827 Taking the results from Round 1 Chains 5, Residues 448, Estimated correctness of the model 97.8 % 4 chains (447 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 138 B and 141 B Built loop between residues 185 B and 188 B 2 chains (451 residues) following loop building 2 chains (451 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4328 restraints for refining 4510 atoms. 603 conditional restraints added. Observations/parameters ratio is 4.14 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1955 (Rfree = 0.000) for 4510 atoms. Found 169 (169 requested) and removed 31 (92 requested) atoms. Cycle 22: After refmac, R = 0.1824 (Rfree = 0.000) for 4643 atoms. Found 174 (174 requested) and removed 46 (94 requested) atoms. Cycle 23: After refmac, R = 0.1760 (Rfree = 0.000) for 4758 atoms. Found 165 (178 requested) and removed 56 (97 requested) atoms. Cycle 24: After refmac, R = 0.1729 (Rfree = 0.000) for 4852 atoms. Found 140 (182 requested) and removed 88 (99 requested) atoms. Cycle 25: After refmac, R = 0.1699 (Rfree = 0.000) for 4885 atoms. Found 166 (180 requested) and removed 82 (100 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4969 seeds are put forward Round 1: 452 peptides, 3 chains. Longest chain 227 peptides. Score 0.836 Round 2: 448 peptides, 7 chains. Longest chain 152 peptides. Score 0.817 Round 3: 449 peptides, 5 chains. Longest chain 138 peptides. Score 0.826 Round 4: 449 peptides, 7 chains. Longest chain 138 peptides. Score 0.818 Round 5: 448 peptides, 7 chains. Longest chain 138 peptides. Score 0.817 Taking the results from Round 1 Chains 3, Residues 449, Estimated correctness of the model 97.9 % 3 chains (449 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 190 B and 193 B 2 chains (451 residues) following loop building 2 chains (451 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4338 restraints for refining 4550 atoms. 613 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1804 (Rfree = 0.000) for 4550 atoms. Found 166 (166 requested) and removed 25 (92 requested) atoms. Cycle 27: After refmac, R = 0.1755 (Rfree = 0.000) for 4676 atoms. Found 172 (172 requested) and removed 64 (95 requested) atoms. Cycle 28: After refmac, R = 0.1725 (Rfree = 0.000) for 4765 atoms. Found 154 (175 requested) and removed 58 (97 requested) atoms. Cycle 29: After refmac, R = 0.1707 (Rfree = 0.000) for 4845 atoms. Found 157 (178 requested) and removed 84 (99 requested) atoms. Cycle 30: After refmac, R = 0.1695 (Rfree = 0.000) for 4895 atoms. Found 176 (176 requested) and removed 86 (100 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4986 seeds are put forward Round 1: 450 peptides, 4 chains. Longest chain 226 peptides. Score 0.831 Round 2: 447 peptides, 7 chains. Longest chain 150 peptides. Score 0.816 Round 3: 448 peptides, 7 chains. Longest chain 214 peptides. Score 0.817 Round 4: 447 peptides, 6 chains. Longest chain 151 peptides. Score 0.821 Round 5: 448 peptides, 6 chains. Longest chain 96 peptides. Score 0.821 Taking the results from Round 1 Chains 4, Residues 446, Estimated correctness of the model 97.8 % 3 chains (386 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 135 B and 138 B 3 chains (448 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4969 restraints for refining 4534 atoms. 1535 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1859 (Rfree = 0.000) for 4534 atoms. Found 163 (163 requested) and removed 28 (92 requested) atoms. Cycle 32: After refmac, R = 0.1767 (Rfree = 0.000) for 4653 atoms. Found 167 (167 requested) and removed 31 (95 requested) atoms. Cycle 33: After refmac, R = 0.1712 (Rfree = 0.000) for 4773 atoms. Found 150 (172 requested) and removed 55 (97 requested) atoms. Cycle 34: After refmac, R = 0.1695 (Rfree = 0.000) for 4856 atoms. Found 147 (174 requested) and removed 72 (99 requested) atoms. Cycle 35: After refmac, R = 0.1691 (Rfree = 0.000) for 4912 atoms. Found 151 (177 requested) and removed 93 (100 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.03 1.51 NCS extension: 3 residues added (223 deleted due to clashes), 4973 seeds are put forward Round 1: 453 peptides, 2 chains. Longest chain 227 peptides. Score 0.841 Round 2: 450 peptides, 5 chains. Longest chain 227 peptides. Score 0.827 Round 3: 449 peptides, 7 chains. Longest chain 138 peptides. Score 0.818 Round 4: 449 peptides, 5 chains. Longest chain 150 peptides. Score 0.826 Round 5: 446 peptides, 8 chains. Longest chain 111 peptides. Score 0.811 Taking the results from Round 1 Chains 2, Residues 451, Estimated correctness of the model 98.0 % 2 chains (451 residues) have been docked in sequence Building loops using Loopy2018 2 chains (451 residues) following loop building 2 chains (451 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4414 restraints for refining 4557 atoms. 689 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1807 (Rfree = 0.000) for 4557 atoms. Found 160 (160 requested) and removed 28 (93 requested) atoms. Cycle 37: After refmac, R = 0.1732 (Rfree = 0.000) for 4672 atoms. Found 164 (164 requested) and removed 50 (95 requested) atoms. Cycle 38: After refmac, R = 0.1712 (Rfree = 0.000) for 4771 atoms. Found 168 (168 requested) and removed 54 (97 requested) atoms. Cycle 39: After refmac, R = 0.1686 (Rfree = 0.000) for 4876 atoms. Found 139 (171 requested) and removed 79 (99 requested) atoms. Cycle 40: After refmac, R = 0.1668 (Rfree = 0.000) for 4907 atoms. Found 168 (169 requested) and removed 81 (100 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4994 seeds are put forward Round 1: 449 peptides, 3 chains. Longest chain 226 peptides. Score 0.834 Round 2: 448 peptides, 7 chains. Longest chain 150 peptides. Score 0.817 Round 3: 451 peptides, 4 chains. Longest chain 226 peptides. Score 0.832 Round 4: 448 peptides, 9 chains. Longest chain 83 peptides. Score 0.809 Round 5: 447 peptides, 9 chains. Longest chain 111 peptides. Score 0.808 Taking the results from Round 1 Chains 3, Residues 446, Estimated correctness of the model 97.8 % 3 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (448 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4362 restraints for refining 4540 atoms. 656 conditional restraints added. Observations/parameters ratio is 4.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1815 (Rfree = 0.000) for 4540 atoms. Found 155 (155 requested) and removed 29 (92 requested) atoms. Cycle 42: After refmac, R = 0.1755 (Rfree = 0.000) for 4648 atoms. Found 160 (160 requested) and removed 41 (95 requested) atoms. Cycle 43: After refmac, R = 0.1702 (Rfree = 0.000) for 4749 atoms. Found 163 (163 requested) and removed 64 (97 requested) atoms. Cycle 44: After refmac, R = 0.1686 (Rfree = 0.000) for 4828 atoms. Found 141 (166 requested) and removed 80 (99 requested) atoms. Cycle 45: After refmac, R = 0.1678 (Rfree = 0.000) for 4870 atoms. Found 163 (163 requested) and removed 83 (99 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4950 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 448 peptides, 7 chains. Longest chain 150 peptides. Score 0.817 Round 3: 449 peptides, 5 chains. Longest chain 138 peptides. Score 0.826 Round 4: 448 peptides, 8 chains. Longest chain 138 peptides. Score 0.813 Round 5: 447 peptides, 8 chains. Longest chain 111 peptides. Score 0.812 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 448, Estimated correctness of the model 97.9 % 3 chains (448 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 74702 reflections ( 94.58 % complete ) and 3718 restraints for refining 3614 atoms. Observations/parameters ratio is 5.17 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2402 (Rfree = 0.000) for 3614 atoms. Found 118 (118 requested) and removed 0 (118 requested) atoms. Cycle 47: After refmac, R = 0.2193 (Rfree = 0.000) for 3614 atoms. Found 122 (122 requested) and removed 3 (76 requested) atoms. Cycle 48: After refmac, R = 0.2008 (Rfree = 0.000) for 3614 atoms. Found 109 (126 requested) and removed 2 (78 requested) atoms. Cycle 49: After refmac, R = 0.1895 (Rfree = 0.000) for 3614 atoms. TimeTaking 1231.53