Sun 23 Dec 22:22:59 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 1vk8-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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/1vk8-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 22:23:07 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/1vk8-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 284 and 0 Target number of residues in the AU: 284 Target solvent content: 0.5942 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-3.2-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.55 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 3 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: 41.711 3.200 Wilson plot Bfac: 50.12 5809 reflections ( 96.00 % complete ) and 0 restraints for refining 3766 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.2955 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2179 (Rfree = 0.000) for 3766 atoms. Found 17 (33 requested) and removed 35 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 3.45 Search for helices and strands: 0 residues in 0 chains, 3827 seeds are put forward NCS extension: 0 residues added, 3827 seeds are put forward Round 1: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.450 Round 2: 208 peptides, 29 chains. Longest chain 17 peptides. Score 0.560 Round 3: 232 peptides, 27 chains. Longest chain 23 peptides. Score 0.661 Round 4: 236 peptides, 27 chains. Longest chain 23 peptides. Score 0.671 Round 5: 247 peptides, 24 chains. Longest chain 33 peptides. Score 0.732 Taking the results from Round 5 Chains 24, Residues 223, Estimated correctness of the model 71.7 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 24 chains (223 residues) following loop building 3 chains (65 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 5969 restraints for refining 3095 atoms. 4814 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2134 (Rfree = 0.000) for 3095 atoms. Found 13 (27 requested) and removed 36 (13 requested) atoms. Cycle 2: After refmac, R = 0.1949 (Rfree = 0.000) for 3028 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.1908 (Rfree = 0.000) for 3002 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.1869 (Rfree = 0.000) for 2986 atoms. Found 10 (24 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.1798 (Rfree = 0.000) for 2975 atoms. Found 3 (24 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 3073 seeds are put forward NCS extension: 18 residues added (11 deleted due to clashes), 3091 seeds are put forward Round 1: 231 peptides, 29 chains. Longest chain 17 peptides. Score 0.632 Round 2: 245 peptides, 25 chains. Longest chain 31 peptides. Score 0.717 Round 3: 256 peptides, 26 chains. Longest chain 26 peptides. Score 0.731 Round 4: 262 peptides, 31 chains. Longest chain 34 peptides. Score 0.691 Round 5: 265 peptides, 25 chains. Longest chain 40 peptides. Score 0.760 Taking the results from Round 5 Chains 29, Residues 240, Estimated correctness of the model 76.9 % 2 chains (53 residues) have been docked in sequence Building loops using Loopy2018 29 chains (240 residues) following loop building 2 chains (53 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6103 restraints for refining 3071 atoms. 4952 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 3071 atoms. Found 19 (24 requested) and removed 34 (13 requested) atoms. Cycle 7: After refmac, R = 0.1806 (Rfree = 0.000) for 3031 atoms. Found 8 (24 requested) and removed 20 (13 requested) atoms. Cycle 8: After refmac, R = 0.1690 (Rfree = 0.000) for 3016 atoms. Found 7 (23 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.1637 (Rfree = 0.000) for 2999 atoms. Found 4 (22 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.1660 (Rfree = 0.000) for 2982 atoms. Found 7 (21 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 3095 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3109 seeds are put forward Round 1: 199 peptides, 30 chains. Longest chain 15 peptides. Score 0.513 Round 2: 234 peptides, 28 chains. Longest chain 34 peptides. Score 0.654 Round 3: 249 peptides, 27 chains. Longest chain 35 peptides. Score 0.704 Round 4: 248 peptides, 30 chains. Longest chain 35 peptides. Score 0.667 Round 5: 234 peptides, 26 chains. Longest chain 30 peptides. Score 0.678 Taking the results from Round 3 Chains 30, Residues 222, Estimated correctness of the model 66.0 % 2 chains (46 residues) have been docked in sequence Building loops using Loopy2018 30 chains (222 residues) following loop building 2 chains (46 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6322 restraints for refining 3066 atoms. 5260 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1883 (Rfree = 0.000) for 3066 atoms. Found 11 (22 requested) and removed 28 (13 requested) atoms. Cycle 12: After refmac, R = 0.1756 (Rfree = 0.000) for 3040 atoms. Found 4 (21 requested) and removed 17 (13 requested) atoms. Cycle 13: After refmac, R = 0.1717 (Rfree = 0.000) for 3025 atoms. Found 4 (21 requested) and removed 14 (13 requested) atoms. Cycle 14: After refmac, R = 0.1724 (Rfree = 0.000) for 3013 atoms. Found 2 (20 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.1715 (Rfree = 0.000) for 3001 atoms. Found 2 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 3.49 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 16 residues added (17 deleted due to clashes), 3125 seeds are put forward Round 1: 218 peptides, 32 chains. Longest chain 15 peptides. Score 0.549 Round 2: 249 peptides, 34 chains. Longest chain 30 peptides. Score 0.620 Round 3: 253 peptides, 27 chains. Longest chain 29 peptides. Score 0.714 Round 4: 247 peptides, 34 chains. Longest chain 19 peptides. Score 0.614 Round 5: 259 peptides, 30 chains. Longest chain 29 peptides. Score 0.695 Taking the results from Round 3 Chains 29, Residues 226, Estimated correctness of the model 68.1 % 2 chains (36 residues) have been docked in sequence Building loops using Loopy2018 29 chains (226 residues) following loop building 2 chains (36 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6465 restraints for refining 3059 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1927 (Rfree = 0.000) for 3059 atoms. Found 15 (19 requested) and removed 19 (13 requested) atoms. Cycle 17: After refmac, R = 0.1735 (Rfree = 0.000) for 3052 atoms. Found 6 (18 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.1635 (Rfree = 0.000) for 3038 atoms. Found 2 (18 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.1600 (Rfree = 0.000) for 3025 atoms. Found 4 (17 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.1590 (Rfree = 0.000) for 3014 atoms. Found 4 (17 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 3.48 Search for helices and strands: 0 residues in 0 chains, 3126 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 3154 seeds are put forward Round 1: 213 peptides, 33 chains. Longest chain 18 peptides. Score 0.517 Round 2: 240 peptides, 28 chains. Longest chain 23 peptides. Score 0.670 Round 3: 239 peptides, 29 chains. Longest chain 24 peptides. Score 0.655 Round 4: 250 peptides, 30 chains. Longest chain 27 peptides. Score 0.672 Round 5: 238 peptides, 30 chains. Longest chain 34 peptides. Score 0.640 Taking the results from Round 4 Chains 32, Residues 220, Estimated correctness of the model 59.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6813 restraints for refining 3067 atoms. 5910 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1842 (Rfree = 0.000) for 3067 atoms. Found 16 (16 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.1712 (Rfree = 0.000) for 3060 atoms. Found 7 (16 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.1703 (Rfree = 0.000) for 3049 atoms. Found 6 (16 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.1659 (Rfree = 0.000) for 3040 atoms. Found 6 (16 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.1636 (Rfree = 0.000) for 3029 atoms. Found 9 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.51 Search for helices and strands: 0 residues in 0 chains, 3140 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3156 seeds are put forward Round 1: 205 peptides, 32 chains. Longest chain 14 peptides. Score 0.504 Round 2: 243 peptides, 30 chains. Longest chain 23 peptides. Score 0.653 Round 3: 233 peptides, 31 chains. Longest chain 22 peptides. Score 0.612 Round 4: 228 peptides, 28 chains. Longest chain 23 peptides. Score 0.637 Round 5: 224 peptides, 29 chains. Longest chain 21 peptides. Score 0.611 Taking the results from Round 2 Chains 30, Residues 213, Estimated correctness of the model 54.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6991 restraints for refining 3060 atoms. 6169 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1660 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 14 (13 requested) atoms. Cycle 27: After refmac, R = 0.1527 (Rfree = 0.000) for 3060 atoms. Found 2 (16 requested) and removed 14 (13 requested) atoms. Cycle 28: After refmac, R = 0.1462 (Rfree = 0.000) for 3046 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.1563 (Rfree = 0.000) for 3036 atoms. Found 6 (16 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.1420 (Rfree = 0.000) for 3028 atoms. Found 2 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 11 residues added (10 deleted due to clashes), 3120 seeds are put forward Round 1: 197 peptides, 32 chains. Longest chain 15 peptides. Score 0.474 Round 2: 208 peptides, 29 chains. Longest chain 23 peptides. Score 0.560 Round 3: 194 peptides, 29 chains. Longest chain 15 peptides. Score 0.511 Round 4: 220 peptides, 29 chains. Longest chain 25 peptides. Score 0.599 Round 5: 210 peptides, 32 chains. Longest chain 15 peptides. Score 0.522 Taking the results from Round 4 Chains 29, Residues 191, Estimated correctness of the model 40.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 7236 restraints for refining 3080 atoms. 6501 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1733 (Rfree = 0.000) for 3080 atoms. Found 15 (16 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.1572 (Rfree = 0.000) for 3074 atoms. Found 6 (16 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.1551 (Rfree = 0.000) for 3063 atoms. Found 5 (16 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1516 (Rfree = 0.000) for 3053 atoms. Found 3 (16 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1490 (Rfree = 0.000) for 3043 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 3132 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3147 seeds are put forward Round 1: 184 peptides, 31 chains. Longest chain 15 peptides. Score 0.440 Round 2: 213 peptides, 33 chains. Longest chain 16 peptides. Score 0.517 Round 3: 208 peptides, 30 chains. Longest chain 16 peptides. Score 0.545 Round 4: 216 peptides, 30 chains. Longest chain 17 peptides. Score 0.572 Round 5: 203 peptides, 28 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 4 Chains 30, Residues 186, Estimated correctness of the model 33.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 7114 restraints for refining 3077 atoms. 6400 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1661 (Rfree = 0.000) for 3077 atoms. Found 13 (16 requested) and removed 13 (13 requested) atoms. Cycle 37: After refmac, R = 0.1497 (Rfree = 0.000) for 3072 atoms. Found 9 (16 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.1414 (Rfree = 0.000) for 3065 atoms. Found 2 (16 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1353 (Rfree = 0.000) for 3053 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1415 (Rfree = 0.000) for 3043 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 3129 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3146 seeds are put forward Round 1: 166 peptides, 30 chains. Longest chain 16 peptides. Score 0.383 Round 2: 192 peptides, 26 chains. Longest chain 16 peptides. Score 0.551 Round 3: 190 peptides, 25 chains. Longest chain 16 peptides. Score 0.560 Round 4: 202 peptides, 26 chains. Longest chain 19 peptides. Score 0.585 Round 5: 194 peptides, 26 chains. Longest chain 24 peptides. Score 0.558 Taking the results from Round 4 Chains 27, Residues 176, Estimated correctness of the model 37.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6874 restraints for refining 3096 atoms. 6066 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1654 (Rfree = 0.000) for 3096 atoms. Found 16 (16 requested) and removed 21 (13 requested) atoms. Cycle 42: After refmac, R = 0.1606 (Rfree = 0.000) for 3088 atoms. Found 10 (16 requested) and removed 14 (13 requested) atoms. Cycle 43: After refmac, R = 0.1455 (Rfree = 0.000) for 3081 atoms. Found 10 (16 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.1355 (Rfree = 0.000) for 3069 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1412 (Rfree = 0.000) for 3059 atoms. Found 15 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 3148 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3171 seeds are put forward Round 1: 141 peptides, 27 chains. Longest chain 15 peptides. Score 0.329 Round 2: 180 peptides, 29 chains. Longest chain 15 peptides. Score 0.458 Round 3: 166 peptides, 23 chains. Longest chain 19 peptides. Score 0.506 Round 4: 160 peptides, 23 chains. Longest chain 20 peptides. Score 0.483 Round 5: 169 peptides, 24 chains. Longest chain 20 peptides. Score 0.500 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 143, Estimated correctness of the model 13.3 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5809 reflections ( 96.00 % complete ) and 7197 restraints for refining 3086 atoms. 6610 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1504 (Rfree = 0.000) for 3086 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1458 (Rfree = 0.000) for 3069 atoms. Found 0 (16 requested) and removed 3 (13 requested) atoms. Cycle 48: After refmac, R = 0.1408 (Rfree = 0.000) for 3066 atoms. Found 0 (16 requested) and removed 8 (13 requested) atoms. Cycle 49: After refmac, R = 0.1354 (Rfree = 0.000) for 3056 atoms. TimeTaking 53.72