null Sun 23 Dec 22:22:43 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 1zkg-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-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/1zkg-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-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 22:22:52 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/1zkg-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-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 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.6389 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-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: 4 Cell parameters: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-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 0.75 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 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: 29.148 3.200 Wilson plot Bfac: 71.17 7991 reflections ( 99.85 % complete ) and 0 restraints for refining 3760 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3319 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3026 (Rfree = 0.000) for 3760 atoms. Found 33 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.17 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 0 residues added, 3884 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 8 peptides. Score 0.292 Round 2: 217 peptides, 38 chains. Longest chain 10 peptides. Score 0.403 Round 3: 232 peptides, 34 chains. Longest chain 21 peptides. Score 0.502 Round 4: 237 peptides, 32 chains. Longest chain 15 peptides. Score 0.541 Round 5: 256 peptides, 32 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 5 Chains 32, Residues 224, Estimated correctness of the model 38.6 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6808 restraints for refining 3096 atoms. 5847 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2633 (Rfree = 0.000) for 3096 atoms. Found 22 (27 requested) and removed 23 (13 requested) atoms. Cycle 2: After refmac, R = 0.2553 (Rfree = 0.000) for 3056 atoms. Found 16 (27 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2606 (Rfree = 0.000) for 3018 atoms. Found 17 (27 requested) and removed 21 (13 requested) atoms. Cycle 4: After refmac, R = 0.2383 (Rfree = 0.000) for 2997 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2172 (Rfree = 0.000) for 2986 atoms. Found 8 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 3132 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3157 seeds are put forward Round 1: 228 peptides, 37 chains. Longest chain 30 peptides. Score 0.451 Round 2: 253 peptides, 31 chains. Longest chain 33 peptides. Score 0.595 Round 3: 263 peptides, 35 chains. Longest chain 28 peptides. Score 0.575 Round 4: 277 peptides, 33 chains. Longest chain 34 peptides. Score 0.631 Round 5: 276 peptides, 35 chains. Longest chain 32 peptides. Score 0.607 Taking the results from Round 4 Chains 34, Residues 244, Estimated correctness of the model 49.1 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6492 restraints for refining 3064 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2582 (Rfree = 0.000) for 3064 atoms. Found 23 (27 requested) and removed 25 (13 requested) atoms. Cycle 7: After refmac, R = 0.2522 (Rfree = 0.000) for 3039 atoms. Found 25 (27 requested) and removed 31 (13 requested) atoms. Cycle 8: After refmac, R = 0.2295 (Rfree = 0.000) for 3017 atoms. Found 14 (27 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.2195 (Rfree = 0.000) for 3005 atoms. Found 13 (27 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.2008 (Rfree = 0.000) for 2999 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 3144 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3162 seeds are put forward Round 1: 240 peptides, 38 chains. Longest chain 18 peptides. Score 0.474 Round 2: 265 peptides, 36 chains. Longest chain 27 peptides. Score 0.568 Round 3: 254 peptides, 32 chains. Longest chain 33 peptides. Score 0.586 Round 4: 267 peptides, 38 chains. Longest chain 21 peptides. Score 0.551 Round 5: 243 peptides, 32 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 3 Chains 32, Residues 222, Estimated correctness of the model 37.2 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6651 restraints for refining 3096 atoms. 5715 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2534 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 12: After refmac, R = 0.2149 (Rfree = 0.000) for 3092 atoms. Found 16 (27 requested) and removed 17 (13 requested) atoms. Cycle 13: After refmac, R = 0.2120 (Rfree = 0.000) for 3087 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 3082 atoms. Found 12 (27 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.1995 (Rfree = 0.000) for 3074 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 64 residues added (9 deleted due to clashes), 3314 seeds are put forward Round 1: 239 peptides, 39 chains. Longest chain 21 peptides. Score 0.458 Round 2: 254 peptides, 35 chains. Longest chain 19 peptides. Score 0.551 Round 3: 258 peptides, 34 chains. Longest chain 30 peptides. Score 0.573 Round 4: 256 peptides, 32 chains. Longest chain 31 peptides. Score 0.591 Round 5: 251 peptides, 37 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 4 Chains 33, Residues 224, Estimated correctness of the model 38.6 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6554 restraints for refining 3096 atoms. 5588 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2338 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 17: After refmac, R = 0.2169 (Rfree = 0.000) for 3093 atoms. Found 12 (27 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.2169 (Rfree = 0.000) for 3085 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 3078 atoms. Found 13 (27 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.2017 (Rfree = 0.000) for 3073 atoms. Found 7 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3207 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3228 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 14 peptides. Score 0.408 Round 2: 254 peptides, 36 chains. Longest chain 24 peptides. Score 0.539 Round 3: 257 peptides, 37 chains. Longest chain 31 peptides. Score 0.535 Round 4: 250 peptides, 37 chains. Longest chain 26 peptides. Score 0.516 Round 5: 262 peptides, 35 chains. Longest chain 23 peptides. Score 0.572 Taking the results from Round 5 Chains 36, Residues 227, Estimated correctness of the model 33.3 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6397 restraints for refining 3096 atoms. 5360 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2277 (Rfree = 0.000) for 3096 atoms. Found 23 (27 requested) and removed 16 (13 requested) atoms. Cycle 22: After refmac, R = 0.2245 (Rfree = 0.000) for 3090 atoms. Found 16 (27 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2042 (Rfree = 0.000) for 3081 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2094 (Rfree = 0.000) for 3068 atoms. Found 14 (27 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.1965 (Rfree = 0.000) for 3067 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3228 seeds are put forward Round 1: 223 peptides, 43 chains. Longest chain 12 peptides. Score 0.352 Round 2: 236 peptides, 39 chains. Longest chain 17 peptides. Score 0.449 Round 3: 231 peptides, 34 chains. Longest chain 24 peptides. Score 0.499 Round 4: 238 peptides, 34 chains. Longest chain 22 peptides. Score 0.520 Round 5: 234 peptides, 33 chains. Longest chain 32 peptides. Score 0.521 Taking the results from Round 5 Chains 35, Residues 201, Estimated correctness of the model 18.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6646 restraints for refining 3096 atoms. 5793 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2257 (Rfree = 0.000) for 3096 atoms. Found 24 (27 requested) and removed 14 (13 requested) atoms. Cycle 27: After refmac, R = 0.2045 (Rfree = 0.000) for 3097 atoms. Found 11 (27 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.1996 (Rfree = 0.000) for 3089 atoms. Found 10 (27 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.1912 (Rfree = 0.000) for 3078 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1880 (Rfree = 0.000) for 3068 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3219 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3236 seeds are put forward Round 1: 190 peptides, 36 chains. Longest chain 17 peptides. Score 0.341 Round 2: 218 peptides, 37 chains. Longest chain 15 peptides. Score 0.420 Round 3: 234 peptides, 35 chains. Longest chain 22 peptides. Score 0.495 Round 4: 223 peptides, 32 chains. Longest chain 32 peptides. Score 0.502 Round 5: 227 peptides, 34 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 4 Chains 34, Residues 191, Estimated correctness of the model 12.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6603 restraints for refining 3096 atoms. 5748 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2403 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 32: After refmac, R = 0.2004 (Rfree = 0.000) for 3077 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. Cycle 33: After refmac, R = 0.1996 (Rfree = 0.000) for 3069 atoms. Found 11 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.1929 (Rfree = 0.000) for 3059 atoms. Found 13 (27 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1748 (Rfree = 0.000) for 3054 atoms. Found 7 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3244 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 16 peptides. Score 0.317 Round 2: 218 peptides, 37 chains. Longest chain 16 peptides. Score 0.420 Round 3: 217 peptides, 37 chains. Longest chain 13 peptides. Score 0.417 Round 4: 218 peptides, 36 chains. Longest chain 13 peptides. Score 0.434 Round 5: 213 peptides, 35 chains. Longest chain 13 peptides. Score 0.432 Taking the results from Round 4 Chains 36, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6985 restraints for refining 3096 atoms. 6293 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2243 (Rfree = 0.000) for 3096 atoms. Found 23 (27 requested) and removed 16 (13 requested) atoms. Cycle 37: After refmac, R = 0.2031 (Rfree = 0.000) for 3097 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. Cycle 38: After refmac, R = 0.2005 (Rfree = 0.000) for 3091 atoms. Found 8 (27 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1960 (Rfree = 0.000) for 3083 atoms. Found 9 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1938 (Rfree = 0.000) for 3077 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3257 seeds are put forward Round 1: 175 peptides, 32 chains. Longest chain 16 peptides. Score 0.348 Round 2: 211 peptides, 32 chains. Longest chain 16 peptides. Score 0.466 Round 3: 200 peptides, 35 chains. Longest chain 14 peptides. Score 0.389 Round 4: 216 peptides, 36 chains. Longest chain 14 peptides. Score 0.427 Round 5: 207 peptides, 34 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 2 Chains 32, Residues 179, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6921 restraints for refining 3095 atoms. 6220 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2131 (Rfree = 0.000) for 3095 atoms. Found 20 (27 requested) and removed 14 (13 requested) atoms. Cycle 42: After refmac, R = 0.2025 (Rfree = 0.000) for 3094 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.1940 (Rfree = 0.000) for 3091 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1887 (Rfree = 0.000) for 3082 atoms. Found 7 (27 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1848 (Rfree = 0.000) for 3073 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 3216 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 7 peptides. Score 0.262 Round 2: 177 peptides, 31 chains. Longest chain 13 peptides. Score 0.370 Round 3: 168 peptides, 31 chains. Longest chain 9 peptides. Score 0.338 Round 4: 179 peptides, 31 chains. Longest chain 15 peptides. Score 0.377 Round 5: 173 peptides, 29 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1zkg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.85 % complete ) and 7076 restraints for refining 3096 atoms. 6529 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1986 (Rfree = 0.000) for 3096 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2031 (Rfree = 0.000) for 3076 atoms. Found 0 (27 requested) and removed 8 (13 requested) atoms. Cycle 48: After refmac, R = 0.1909 (Rfree = 0.000) for 3064 atoms. Found 0 (27 requested) and removed 4 (13 requested) atoms. Cycle 49: After refmac, R = 0.1931 (Rfree = 0.000) for 3058 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:01 GMT 2018 Job finished. TimeTaking 53.32 Used memory is bytes: 7952192