Mon 24 Dec 07:52:02 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 2fur-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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/2fur-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 07:52:07 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 372 and 0 Target number of residues in the AU: 372 Target solvent content: 0.5051 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-1.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.40 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: 55.473 1.798 Wilson plot Bfac: 24.57 38188 reflections ( 99.31 % complete ) and 0 restraints for refining 3699 atoms. Observations/parameters ratio is 2.58 ------------------------------------------------------ Starting model: R = 0.3456 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3013 (Rfree = 0.000) for 3699 atoms. Found 92 (171 requested) and removed 102 (85 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 2.26 NCS extension: 0 residues added, 3689 seeds are put forward Round 1: 260 peptides, 32 chains. Longest chain 22 peptides. Score 0.654 Round 2: 318 peptides, 24 chains. Longest chain 31 peptides. Score 0.833 Round 3: 338 peptides, 22 chains. Longest chain 49 peptides. Score 0.868 Round 4: 350 peptides, 12 chains. Longest chain 90 peptides. Score 0.925 Round 5: 352 peptides, 10 chains. Longest chain 129 peptides. Score 0.934 Taking the results from Round 5 Chains 13, Residues 342, Estimated correctness of the model 99.7 % 7 chains (310 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 145 A and 150 A Built loop between residues 169 A and 177 A Built loop between residues 38 B and 43 B 8 chains (354 residues) following loop building 4 chains (325 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3603 restraints for refining 3328 atoms. 884 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3317 (Rfree = 0.000) for 3328 atoms. Found 105 (154 requested) and removed 85 (77 requested) atoms. Cycle 2: After refmac, R = 0.2942 (Rfree = 0.000) for 3342 atoms. Found 87 (152 requested) and removed 42 (77 requested) atoms. Cycle 3: After refmac, R = 0.2753 (Rfree = 0.000) for 3358 atoms. Found 73 (154 requested) and removed 25 (78 requested) atoms. Cycle 4: After refmac, R = 0.2611 (Rfree = 0.000) for 3391 atoms. Found 59 (155 requested) and removed 9 (79 requested) atoms. Cycle 5: After refmac, R = 0.2506 (Rfree = 0.000) for 3430 atoms. Found 56 (156 requested) and removed 18 (79 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.02 2.19 NCS extension: 42 residues added (97 deleted due to clashes), 3514 seeds are put forward Round 1: 370 peptides, 8 chains. Longest chain 135 peptides. Score 0.949 Round 2: 375 peptides, 5 chains. Longest chain 149 peptides. Score 0.961 Round 3: 378 peptides, 4 chains. Longest chain 191 peptides. Score 0.965 Round 4: 369 peptides, 9 chains. Longest chain 149 peptides. Score 0.946 Round 5: 376 peptides, 7 chains. Longest chain 139 peptides. Score 0.955 Taking the results from Round 3 Chains 5, Residues 374, Estimated correctness of the model 99.9 % 4 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 42 B Built loop between residues 148 B and 151 B 3 chains (377 residues) following loop building 3 chains (377 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3273 restraints for refining 3401 atoms. 243 conditional restraints added. Observations/parameters ratio is 2.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2579 (Rfree = 0.000) for 3401 atoms. Found 98 (154 requested) and removed 65 (78 requested) atoms. Cycle 7: After refmac, R = 0.2355 (Rfree = 0.000) for 3431 atoms. Found 81 (153 requested) and removed 20 (79 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 3485 atoms. Found 62 (156 requested) and removed 20 (81 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 3518 atoms. Found 63 (156 requested) and removed 22 (81 requested) atoms. Cycle 10: After refmac, R = 0.2065 (Rfree = 0.000) for 3555 atoms. Found 63 (158 requested) and removed 34 (82 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 2.17 NCS extension: 0 residues added, 3586 seeds are put forward Round 1: 379 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 378 peptides, 4 chains. Longest chain 191 peptides. Score 0.965 Round 3: 381 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 4: 375 peptides, 4 chains. Longest chain 157 peptides. Score 0.964 Round 5: 380 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Taking the results from Round 3 Chains 3, Residues 379, Estimated correctness of the model 99.9 % 2 chains (378 residues) have been docked in sequence Building loops using Loopy2018 3 chains (379 residues) following loop building 3 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3265 restraints for refining 3446 atoms. 216 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2195 (Rfree = 0.000) for 3446 atoms. Found 109 (149 requested) and removed 57 (79 requested) atoms. Cycle 12: After refmac, R = 0.2092 (Rfree = 0.000) for 3492 atoms. Found 83 (149 requested) and removed 25 (81 requested) atoms. Cycle 13: After refmac, R = 0.2016 (Rfree = 0.000) for 3546 atoms. Found 54 (151 requested) and removed 32 (82 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 3559 atoms. Found 75 (148 requested) and removed 38 (82 requested) atoms. Cycle 15: After refmac, R = 0.1940 (Rfree = 0.000) for 3590 atoms. Found 73 (146 requested) and removed 50 (83 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.00 2.17 NCS extension: 0 residues added, 3614 seeds are put forward Round 1: 379 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Round 2: 377 peptides, 5 chains. Longest chain 156 peptides. Score 0.961 Round 3: 380 peptides, 3 chains. Longest chain 190 peptides. Score 0.968 Round 4: 374 peptides, 5 chains. Longest chain 191 peptides. Score 0.960 Round 5: 376 peptides, 4 chains. Longest chain 138 peptides. Score 0.964 Taking the results from Round 3 Chains 3, Residues 377, Estimated correctness of the model 99.9 % 3 chains (377 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 157 A and 160 A 2 chains (379 residues) following loop building 2 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3281 restraints for refining 3464 atoms. 229 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2112 (Rfree = 0.000) for 3464 atoms. Found 117 (138 requested) and removed 65 (80 requested) atoms. Cycle 17: After refmac, R = 0.2028 (Rfree = 0.000) for 3511 atoms. Found 92 (137 requested) and removed 46 (81 requested) atoms. Cycle 18: After refmac, R = 0.1965 (Rfree = 0.000) for 3555 atoms. Found 82 (139 requested) and removed 42 (82 requested) atoms. Cycle 19: After refmac, R = 0.1930 (Rfree = 0.000) for 3593 atoms. Found 82 (136 requested) and removed 59 (83 requested) atoms. Cycle 20: After refmac, R = 0.1904 (Rfree = 0.000) for 3614 atoms. Found 90 (134 requested) and removed 56 (83 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 2.16 NCS extension: 111 residues added (79 deleted due to clashes), 3760 seeds are put forward Round 1: 380 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 2: 378 peptides, 3 chains. Longest chain 189 peptides. Score 0.968 Round 3: 377 peptides, 3 chains. Longest chain 191 peptides. Score 0.967 Round 4: 376 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 5: 376 peptides, 4 chains. Longest chain 158 peptides. Score 0.964 Taking the results from Round 1 Chains 2, Residues 378, Estimated correctness of the model 99.9 % 2 chains (378 residues) have been docked in sequence Building loops using Loopy2018 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3288 restraints for refining 3473 atoms. 248 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2055 (Rfree = 0.000) for 3473 atoms. Found 120 (126 requested) and removed 56 (80 requested) atoms. Cycle 22: After refmac, R = 0.1988 (Rfree = 0.000) for 3535 atoms. Found 85 (128 requested) and removed 61 (82 requested) atoms. Cycle 23: After refmac, R = 0.1943 (Rfree = 0.000) for 3559 atoms. Found 98 (125 requested) and removed 51 (82 requested) atoms. Cycle 24: After refmac, R = 0.1926 (Rfree = 0.000) for 3606 atoms. Found 89 (124 requested) and removed 70 (83 requested) atoms. Cycle 25: After refmac, R = 0.1895 (Rfree = 0.000) for 3621 atoms. Found 93 (121 requested) and removed 65 (84 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3650 seeds are put forward Round 1: 379 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 381 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 3: 372 peptides, 5 chains. Longest chain 155 peptides. Score 0.960 Round 4: 374 peptides, 5 chains. Longest chain 189 peptides. Score 0.960 Round 5: 380 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 2 Chains 2, Residues 379, Estimated correctness of the model 99.9 % 2 chains (379 residues) have been docked in sequence Building loops using Loopy2018 2 chains (379 residues) following loop building 2 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3279 restraints for refining 3476 atoms. 227 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2029 (Rfree = 0.000) for 3476 atoms. Found 113 (113 requested) and removed 55 (80 requested) atoms. Cycle 27: After refmac, R = 0.1969 (Rfree = 0.000) for 3532 atoms. Found 87 (114 requested) and removed 50 (81 requested) atoms. Cycle 28: After refmac, R = 0.1913 (Rfree = 0.000) for 3567 atoms. Found 90 (112 requested) and removed 49 (82 requested) atoms. Cycle 29: After refmac, R = 0.1894 (Rfree = 0.000) for 3604 atoms. Found 82 (110 requested) and removed 56 (83 requested) atoms. Cycle 30: After refmac, R = 0.1865 (Rfree = 0.000) for 3629 atoms. Found 86 (108 requested) and removed 51 (84 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3665 seeds are put forward Round 1: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 380 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 3: 370 peptides, 5 chains. Longest chain 191 peptides. Score 0.959 Round 4: 372 peptides, 5 chains. Longest chain 122 peptides. Score 0.960 Round 5: 378 peptides, 4 chains. Longest chain 191 peptides. Score 0.965 Taking the results from Round 2 Chains 2, Residues 378, Estimated correctness of the model 99.9 % 2 chains (378 residues) have been docked in sequence Building loops using Loopy2018 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3330 restraints for refining 3505 atoms. 291 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2096 (Rfree = 0.000) for 3505 atoms. Found 100 (100 requested) and removed 66 (81 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 3536 atoms. Found 94 (98 requested) and removed 38 (82 requested) atoms. Cycle 33: After refmac, R = 0.1954 (Rfree = 0.000) for 3588 atoms. Found 76 (100 requested) and removed 67 (83 requested) atoms. Cycle 34: After refmac, R = 0.1911 (Rfree = 0.000) for 3592 atoms. Found 96 (96 requested) and removed 56 (83 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 3632 atoms. Found 81 (94 requested) and removed 67 (84 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3647 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 166 peptides. Score 0.963 Round 2: 376 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 3: 377 peptides, 5 chains. Longest chain 147 peptides. Score 0.961 Round 4: 375 peptides, 3 chains. Longest chain 189 peptides. Score 0.967 Round 5: 377 peptides, 5 chains. Longest chain 139 peptides. Score 0.961 Taking the results from Round 4 Chains 4, Residues 372, Estimated correctness of the model 99.9 % 3 chains (368 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 B and 146 B 3 chains (374 residues) following loop building 2 chains (370 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3395 restraints for refining 3492 atoms. 411 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 3492 atoms. Found 87 (87 requested) and removed 73 (81 requested) atoms. Cycle 37: After refmac, R = 0.1996 (Rfree = 0.000) for 3503 atoms. Found 84 (84 requested) and removed 36 (81 requested) atoms. Cycle 38: After refmac, R = 0.1919 (Rfree = 0.000) for 3551 atoms. Found 85 (85 requested) and removed 43 (82 requested) atoms. Cycle 39: After refmac, R = 0.1871 (Rfree = 0.000) for 3592 atoms. Found 67 (83 requested) and removed 53 (83 requested) atoms. Cycle 40: After refmac, R = 0.1851 (Rfree = 0.000) for 3604 atoms. Found 82 (83 requested) and removed 46 (83 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 2.15 NCS extension: 0 residues added (3 deleted due to clashes), 3641 seeds are put forward Round 1: 376 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 2: 374 peptides, 4 chains. Longest chain 152 peptides. Score 0.963 Round 3: 375 peptides, 6 chains. Longest chain 115 peptides. Score 0.958 Round 4: 372 peptides, 5 chains. Longest chain 152 peptides. Score 0.960 Round 5: 376 peptides, 5 chains. Longest chain 161 peptides. Score 0.961 Taking the results from Round 1 Chains 3, Residues 373, Estimated correctness of the model 99.9 % 3 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 44 B 2 chains (376 residues) following loop building 2 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3336 restraints for refining 3500 atoms. 310 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 3500 atoms. Found 81 (81 requested) and removed 59 (81 requested) atoms. Cycle 42: After refmac, R = 0.1931 (Rfree = 0.000) for 3522 atoms. Found 81 (81 requested) and removed 33 (81 requested) atoms. Cycle 43: After refmac, R = 0.1881 (Rfree = 0.000) for 3570 atoms. Found 72 (82 requested) and removed 40 (82 requested) atoms. Cycle 44: After refmac, R = 0.1850 (Rfree = 0.000) for 3601 atoms. Found 80 (83 requested) and removed 46 (83 requested) atoms. Cycle 45: After refmac, R = 0.1848 (Rfree = 0.000) for 3633 atoms. Found 84 (84 requested) and removed 63 (84 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 2.15 NCS extension: 0 residues added, 3654 seeds are put forward Round 1: 377 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 2: 376 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 3: 376 peptides, 6 chains. Longest chain 147 peptides. Score 0.958 Round 4: 375 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 5: 379 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 376, Estimated correctness of the model 99.9 % 3 chains (375 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 40 B and 44 B 3 chains (379 residues) following loop building 3 chains (379 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38188 reflections ( 99.31 % complete ) and 3049 restraints for refining 2986 atoms. Observations/parameters ratio is 3.20 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2514 (Rfree = 0.000) for 2986 atoms. Found 69 (69 requested) and removed 0 (69 requested) atoms. Cycle 47: After refmac, R = 0.2319 (Rfree = 0.000) for 2986 atoms. Found 36 (70 requested) and removed 0 (70 requested) atoms. Cycle 48: After refmac, R = 0.2181 (Rfree = 0.000) for 2986 atoms. Found 17 (71 requested) and removed 0 (71 requested) atoms. Cycle 49: After refmac, R = 0.2110 (Rfree = 0.000) for 2986 atoms. TimeTaking 52.38