Tue 25 Dec 19:27:57 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 2a2m-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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/2a2m-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 ============================================================ Tue 25 Dec 19:28:07 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/2a2m-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-1.9-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 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-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-1.9-parrot-hancs.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 4576 atoms. Observations/parameters ratio is 4.08 ------------------------------------------------------ Starting model: R = 0.3173 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2663 (Rfree = 0.000) for 4576 atoms. Found 186 (186 requested) and removed 86 (93 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.11 1.57 NCS extension: 0 residues added, 4676 seeds are put forward Round 1: 406 peptides, 37 chains. Longest chain 34 peptides. Score 0.624 Round 2: 427 peptides, 19 chains. Longest chain 97 peptides. Score 0.745 Round 3: 438 peptides, 12 chains. Longest chain 105 peptides. Score 0.788 Round 4: 443 peptides, 9 chains. Longest chain 170 peptides. Score 0.805 Round 5: 440 peptides, 11 chains. Longest chain 87 peptides. Score 0.794 Taking the results from Round 4 Chains 9, Residues 434, Estimated correctness of the model 97.1 % 8 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 81 A Built loop between residues 112 B and 115 B Built loop between residues 121 B and 124 B Built loop between residues 187 B and 190 B Built loop between residues 232 B and 235 B 4 chains (445 residues) following loop building 3 chains (435 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4445 restraints for refining 4411 atoms. 809 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2480 (Rfree = 0.000) for 4411 atoms. Found 180 (180 requested) and removed 40 (90 requested) atoms. Cycle 2: After refmac, R = 0.2113 (Rfree = 0.000) for 4537 atoms. Found 185 (185 requested) and removed 26 (92 requested) atoms. Cycle 3: After refmac, R = 0.1956 (Rfree = 0.000) for 4661 atoms. Found 186 (191 requested) and removed 48 (95 requested) atoms. Cycle 4: After refmac, R = 0.1875 (Rfree = 0.000) for 4761 atoms. Found 156 (196 requested) and removed 57 (98 requested) atoms. Cycle 5: After refmac, R = 0.1809 (Rfree = 0.000) for 4826 atoms. Found 176 (198 requested) and removed 64 (99 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.02 1.50 NCS extension: 3 residues added (241 deleted due to clashes), 4943 seeds are put forward Round 1: 455 peptides, 3 chains. Longest chain 228 peptides. Score 0.838 Round 2: 452 peptides, 7 chains. Longest chain 180 peptides. Score 0.820 Round 3: 451 peptides, 6 chains. Longest chain 128 peptides. Score 0.823 Round 4: 444 peptides, 11 chains. Longest chain 91 peptides. Score 0.797 Round 5: 447 peptides, 11 chains. Longest chain 85 peptides. Score 0.799 Taking the results from Round 1 Chains 3, Residues 452, Estimated correctness of the model 97.9 % 3 chains (452 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (454 residues) following loop building 2 chains (454 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4327 restraints for refining 4532 atoms. 579 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1858 (Rfree = 0.000) for 4532 atoms. Found 185 (185 requested) and removed 31 (92 requested) atoms. Cycle 7: After refmac, R = 0.1786 (Rfree = 0.000) for 4666 atoms. Found 155 (191 requested) and removed 58 (95 requested) atoms. Cycle 8: After refmac, R = 0.1716 (Rfree = 0.000) for 4750 atoms. Found 194 (194 requested) and removed 47 (97 requested) atoms. Cycle 9: After refmac, R = 0.1713 (Rfree = 0.000) for 4873 atoms. Found 147 (200 requested) and removed 106 (100 requested) atoms. Cycle 10: After refmac, R = 0.1680 (Rfree = 0.000) for 4887 atoms. Found 171 (196 requested) and removed 68 (100 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.03 1.51 NCS extension: 0 residues added, 4990 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 445 peptides, 7 chains. Longest chain 152 peptides. Score 0.815 Round 3: 450 peptides, 5 chains. Longest chain 167 peptides. Score 0.827 Round 4: 452 peptides, 7 chains. Longest chain 119 peptides. Score 0.820 Round 5: 450 peptides, 8 chains. Longest chain 100 peptides. Score 0.814 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 4405 restraints for refining 4553 atoms. 687 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1837 (Rfree = 0.000) for 4553 atoms. Found 182 (182 requested) and removed 37 (93 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1779 (Rfree = 0.000) for 4675 atoms. Found 158 (187 requested) and removed 57 (95 requested) atoms. Cycle 13: After refmac, R = 0.1734 (Rfree = 0.000) for 4760 atoms. Found 156 (191 requested) and removed 60 (97 requested) atoms. Cycle 14: After refmac, R = 0.1694 (Rfree = 0.000) for 4835 atoms. Found 155 (194 requested) and removed 67 (99 requested) atoms. Cycle 15: After refmac, R = 0.1689 (Rfree = 0.000) for 4896 atoms. Found 178 (197 requested) and removed 83 (100 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4991 seeds are put forward Round 1: 449 peptides, 3 chains. Longest chain 226 peptides. Score 0.834 Round 2: 443 peptides, 7 chains. Longest chain 151 peptides. Score 0.814 Round 3: 450 peptides, 5 chains. Longest chain 167 peptides. Score 0.827 Round 4: 448 peptides, 5 chains. Longest chain 138 peptides. Score 0.825 Round 5: 449 peptides, 6 chains. Longest chain 150 peptides. Score 0.822 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 4441 restraints for refining 4560 atoms. 735 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1805 (Rfree = 0.000) for 4560 atoms. Found 182 (182 requested) and removed 23 (93 requested) atoms. Cycle 17: After refmac, R = 0.1744 (Rfree = 0.000) for 4702 atoms. Found 170 (188 requested) and removed 69 (96 requested) atoms. Cycle 18: After refmac, R = 0.1717 (Rfree = 0.000) for 4791 atoms. Found 169 (192 requested) and removed 75 (98 requested) atoms. Cycle 19: After refmac, R = 0.1689 (Rfree = 0.000) for 4871 atoms. Found 155 (195 requested) and removed 86 (99 requested) atoms. Cycle 20: After refmac, R = 0.1693 (Rfree = 0.000) for 4917 atoms. Found 149 (193 requested) and removed 98 (100 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4968 seeds are put forward Round 1: 453 peptides, 3 chains. Longest chain 226 peptides. Score 0.837 Round 2: 448 peptides, 6 chains. Longest chain 226 peptides. Score 0.821 Round 3: 450 peptides, 4 chains. Longest chain 226 peptides. Score 0.831 Round 4: 449 peptides, 7 chains. Longest chain 187 peptides. Score 0.818 Round 5: 447 peptides, 12 chains. Longest chain 97 peptides. Score 0.795 Taking the results from Round 1 Chains 3, Residues 450, Estimated correctness of the model 97.9 % 3 chains (450 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 A and 190 A 2 chains (452 residues) following loop building 2 chains (452 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4367 restraints for refining 4553 atoms. 634 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1811 (Rfree = 0.000) for 4553 atoms. Found 175 (175 requested) and removed 33 (93 requested) atoms. Cycle 22: After refmac, R = 0.1746 (Rfree = 0.000) for 4675 atoms. Found 180 (180 requested) and removed 57 (95 requested) atoms. Cycle 23: After refmac, R = 0.1708 (Rfree = 0.000) for 4783 atoms. Found 184 (184 requested) and removed 66 (98 requested) atoms. Cycle 24: After refmac, R = 0.1697 (Rfree = 0.000) for 4882 atoms. Found 167 (188 requested) and removed 97 (100 requested) atoms. Cycle 25: After refmac, R = 0.1698 (Rfree = 0.000) for 4934 atoms. Found 181 (186 requested) and removed 103 (101 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 5012 seeds are put forward Round 1: 451 peptides, 3 chains. Longest chain 226 peptides. Score 0.836 Round 2: 451 peptides, 7 chains. Longest chain 150 peptides. Score 0.819 Round 3: 448 peptides, 5 chains. Longest chain 139 peptides. Score 0.825 Round 4: 446 peptides, 9 chains. Longest chain 83 peptides. Score 0.807 Round 5: 449 peptides, 9 chains. Longest chain 99 peptides. Score 0.809 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 4344 restraints for refining 4543 atoms. 626 conditional restraints added. Observations/parameters ratio is 4.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1797 (Rfree = 0.000) for 4543 atoms. Found 166 (166 requested) and removed 22 (92 requested) atoms. Cycle 27: After refmac, R = 0.1742 (Rfree = 0.000) for 4669 atoms. Found 172 (172 requested) and removed 40 (95 requested) atoms. Cycle 28: After refmac, R = 0.1700 (Rfree = 0.000) for 4785 atoms. Found 169 (176 requested) and removed 75 (98 requested) atoms. Cycle 29: After refmac, R = 0.1706 (Rfree = 0.000) for 4869 atoms. Found 155 (179 requested) and removed 100 (99 requested) atoms. Cycle 30: After refmac, R = 0.1696 (Rfree = 0.000) for 4903 atoms. Found 160 (177 requested) and removed 105 (100 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4958 seeds are put forward Round 1: 454 peptides, 2 chains. Longest chain 228 peptides. Score 0.842 Round 2: 451 peptides, 6 chains. Longest chain 226 peptides. Score 0.823 Round 3: 451 peptides, 6 chains. Longest chain 138 peptides. Score 0.823 Round 4: 447 peptides, 10 chains. Longest chain 167 peptides. Score 0.804 Round 5: 453 peptides, 3 chains. Longest chain 226 peptides. Score 0.837 Taking the results from Round 1 Chains 2, Residues 452, Estimated correctness of the model 98.0 % 2 chains (452 residues) have been docked in sequence Building loops using Loopy2018 2 chains (452 residues) following loop building 2 chains (452 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4317 restraints for refining 4538 atoms. 584 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1812 (Rfree = 0.000) for 4538 atoms. Found 159 (159 requested) and removed 37 (92 requested) atoms. Cycle 32: After refmac, R = 0.1753 (Rfree = 0.000) for 4649 atoms. Found 163 (163 requested) and removed 54 (95 requested) atoms. Cycle 33: After refmac, R = 0.1705 (Rfree = 0.000) for 4742 atoms. Found 167 (167 requested) and removed 55 (97 requested) atoms. Cycle 34: After refmac, R = 0.1691 (Rfree = 0.000) for 4845 atoms. Found 165 (170 requested) and removed 100 (99 requested) atoms. Cycle 35: After refmac, R = 0.1685 (Rfree = 0.000) for 4884 atoms. Found 168 (168 requested) and removed 98 (100 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4954 seeds are put forward Round 1: 453 peptides, 3 chains. Longest chain 226 peptides. Score 0.837 Round 2: 452 peptides, 5 chains. Longest chain 226 peptides. Score 0.828 Round 3: 448 peptides, 8 chains. Longest chain 88 peptides. Score 0.813 Round 4: 454 peptides, 3 chains. Longest chain 229 peptides. Score 0.838 Round 5: 452 peptides, 6 chains. Longest chain 138 peptides. Score 0.824 Taking the results from Round 4 Chains 3, Residues 451, Estimated correctness of the model 97.9 % 3 chains (451 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 B and 71 B 2 chains (453 residues) following loop building 2 chains (453 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4296 restraints for refining 4543 atoms. 554 conditional restraints added. Observations/parameters ratio is 4.11 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1815 (Rfree = 0.000) for 4543 atoms. Found 152 (152 requested) and removed 31 (92 requested) atoms. Cycle 37: After refmac, R = 0.1749 (Rfree = 0.000) for 4652 atoms. Found 156 (156 requested) and removed 43 (95 requested) atoms. Cycle 38: After refmac, R = 0.1705 (Rfree = 0.000) for 4754 atoms. Found 159 (159 requested) and removed 66 (97 requested) atoms. Cycle 39: After refmac, R = 0.1705 (Rfree = 0.000) for 4828 atoms. Found 162 (162 requested) and removed 99 (99 requested) atoms. Cycle 40: After refmac, R = 0.1690 (Rfree = 0.000) for 4870 atoms. Found 159 (159 requested) and removed 83 (99 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4946 seeds are put forward Round 1: 453 peptides, 3 chains. Longest chain 226 peptides. Score 0.837 Round 2: 449 peptides, 6 chains. Longest chain 150 peptides. Score 0.822 Round 3: 451 peptides, 5 chains. Longest chain 138 peptides. Score 0.828 Round 4: 450 peptides, 6 chains. Longest chain 150 peptides. Score 0.823 Round 5: 449 peptides, 10 chains. Longest chain 111 peptides. Score 0.805 Taking the results from Round 1 Chains 3, Residues 450, Estimated correctness of the model 97.9 % 3 chains (450 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 187 B and 190 B 2 chains (452 residues) following loop building 2 chains (452 residues) in sequence following loop building ------------------------------------------------------ 74702 reflections ( 94.58 % complete ) and 4301 restraints for refining 4529 atoms. 568 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1804 (Rfree = 0.000) for 4529 atoms. Found 144 (144 requested) and removed 32 (92 requested) atoms. Cycle 42: After refmac, R = 0.1735 (Rfree = 0.000) for 4633 atoms. Found 147 (147 requested) and removed 45 (94 requested) atoms. Cycle 43: After refmac, R = 0.1707 (Rfree = 0.000) for 4724 atoms. Found 151 (151 requested) and removed 55 (96 requested) atoms. Cycle 44: After refmac, R = 0.1685 (Rfree = 0.000) for 4804 atoms. Found 153 (153 requested) and removed 70 (98 requested) atoms. Cycle 45: After refmac, R = 0.1658 (Rfree = 0.000) for 4862 atoms. Found 155 (155 requested) and removed 87 (99 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 1.50 NCS extension: 0 residues added, 4930 seeds are put forward Round 1: 451 peptides, 4 chains. Longest chain 226 peptides. Score 0.832 Round 2: 451 peptides, 5 chains. Longest chain 150 peptides. Score 0.828 Round 3: 449 peptides, 7 chains. Longest chain 226 peptides. Score 0.818 Round 4: 452 peptides, 7 chains. Longest chain 138 peptides. Score 0.820 Round 5: 444 peptides, 8 chains. Longest chain 152 peptides. Score 0.810 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 447, Estimated correctness of the model 97.8 % 4 chains (447 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 132 A and 135 A Built loop between residues 186 A and 189 A 2 chains (451 residues) following loop building 2 chains (451 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 74702 reflections ( 94.58 % complete ) and 3722 restraints for refining 3618 atoms. Observations/parameters ratio is 5.16 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2402 (Rfree = 0.000) for 3618 atoms. Found 112 (112 requested) and removed 0 (112 requested) atoms. Cycle 47: After refmac, R = 0.2194 (Rfree = 0.000) for 3618 atoms. Found 116 (116 requested) and removed 1 (76 requested) atoms. Cycle 48: After refmac, R = 0.2012 (Rfree = 0.000) for 3618 atoms. Found 119 (119 requested) and removed 9 (78 requested) atoms. Cycle 49: After refmac, R = 0.1907 (Rfree = 0.000) for 3618 atoms. Found 69 (122 requested) and removed 3 (80 requested) atoms. Writing output files ... TimeTaking 1248.67