null Sun 23 Dec 23:54:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.2-parrot-mrncs ############### 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 23:54:15 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-3.2-parrot-mrncs/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 273 and 0 Target number of residues in the AU: 273 Target solvent content: 0.6368 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-3.2-parrot-mrncs.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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.65 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: 55.473 3.200 Wilson plot Bfac: 69.88 7113 reflections ( 99.69 % complete ) and 0 restraints for refining 3710 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3135 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2461 (Rfree = 0.000) for 3710 atoms. Found 16 (33 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3759 seeds are put forward NCS extension: 0 residues added, 3759 seeds are put forward Round 1: 230 peptides, 34 chains. Longest chain 16 peptides. Score 0.541 Round 2: 258 peptides, 29 chains. Longest chain 17 peptides. Score 0.682 Round 3: 274 peptides, 31 chains. Longest chain 24 peptides. Score 0.698 Round 4: 287 peptides, 27 chains. Longest chain 27 peptides. Score 0.763 Round 5: 294 peptides, 25 chains. Longest chain 34 peptides. Score 0.792 Taking the results from Round 5 Chains 28, Residues 269, Estimated correctness of the model 82.2 % 4 chains (71 residues) have been docked in sequence Building loops using Loopy2018 28 chains (269 residues) following loop building 4 chains (71 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 5769 restraints for refining 3050 atoms. 4452 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2730 (Rfree = 0.000) for 3050 atoms. Found 23 (27 requested) and removed 40 (13 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 3010 atoms. Found 8 (26 requested) and removed 19 (13 requested) atoms. Cycle 3: After refmac, R = 0.2495 (Rfree = 0.000) for 2981 atoms. Found 2 (25 requested) and removed 13 (13 requested) atoms. Cycle 4: After refmac, R = 0.2479 (Rfree = 0.000) for 2967 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.2462 (Rfree = 0.000) for 2954 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3004 seeds are put forward NCS extension: 29 residues added (9 deleted due to clashes), 3033 seeds are put forward Round 1: 250 peptides, 36 chains. Longest chain 16 peptides. Score 0.576 Round 2: 277 peptides, 26 chains. Longest chain 27 peptides. Score 0.753 Round 3: 277 peptides, 30 chains. Longest chain 21 peptides. Score 0.715 Round 4: 287 peptides, 23 chains. Longest chain 38 peptides. Score 0.796 Round 5: 280 peptides, 28 chains. Longest chain 25 peptides. Score 0.741 Taking the results from Round 4 Chains 24, Residues 264, Estimated correctness of the model 82.8 % 4 chains (100 residues) have been docked in sequence Building loops using Loopy2018 24 chains (264 residues) following loop building 4 chains (100 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 5627 restraints for refining 3053 atoms. 4211 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2748 (Rfree = 0.000) for 3053 atoms. Found 14 (24 requested) and removed 33 (13 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 3023 atoms. Found 5 (24 requested) and removed 18 (13 requested) atoms. Cycle 8: After refmac, R = 0.2429 (Rfree = 0.000) for 3003 atoms. Found 2 (23 requested) and removed 15 (13 requested) atoms. Cycle 9: After refmac, R = 0.2401 (Rfree = 0.000) for 2988 atoms. Found 2 (22 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.2377 (Rfree = 0.000) for 2974 atoms. Found 2 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward NCS extension: 39 residues added (16 deleted due to clashes), 3078 seeds are put forward Round 1: 258 peptides, 28 chains. Longest chain 38 peptides. Score 0.693 Round 2: 265 peptides, 27 chains. Longest chain 19 peptides. Score 0.719 Round 3: 270 peptides, 27 chains. Longest chain 26 peptides. Score 0.730 Round 4: 281 peptides, 31 chains. Longest chain 31 peptides. Score 0.714 Round 5: 265 peptides, 25 chains. Longest chain 24 peptides. Score 0.739 Taking the results from Round 5 Chains 28, Residues 240, Estimated correctness of the model 73.0 % 2 chains (21 residues) have been docked in sequence Building loops using Loopy2018 28 chains (240 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6604 restraints for refining 3052 atoms. 5592 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2393 (Rfree = 0.000) for 3052 atoms. Found 12 (22 requested) and removed 19 (13 requested) atoms. Cycle 12: After refmac, R = 0.2237 (Rfree = 0.000) for 3040 atoms. Found 8 (21 requested) and removed 13 (13 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 3033 atoms. Found 2 (21 requested) and removed 13 (13 requested) atoms. Cycle 14: After refmac, R = 0.2185 (Rfree = 0.000) for 3020 atoms. Found 8 (20 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.2170 (Rfree = 0.000) for 3015 atoms. Found 1 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3095 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3127 seeds are put forward Round 1: 249 peptides, 32 chains. Longest chain 16 peptides. Score 0.624 Round 2: 266 peptides, 27 chains. Longest chain 35 peptides. Score 0.721 Round 3: 278 peptides, 26 chains. Longest chain 47 peptides. Score 0.755 Round 4: 270 peptides, 27 chains. Longest chain 36 peptides. Score 0.730 Round 5: 270 peptides, 30 chains. Longest chain 23 peptides. Score 0.700 Taking the results from Round 3 Chains 28, Residues 252, Estimated correctness of the model 76.0 % 3 chains (66 residues) have been docked in sequence Building loops using Loopy2018 28 chains (252 residues) following loop building 3 chains (66 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6128 restraints for refining 3052 atoms. 4897 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 3052 atoms. Found 12 (19 requested) and removed 27 (13 requested) atoms. Cycle 17: After refmac, R = 0.2312 (Rfree = 0.000) for 3030 atoms. Found 5 (18 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.2244 (Rfree = 0.000) for 3021 atoms. Found 3 (18 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2208 (Rfree = 0.000) for 3009 atoms. Found 2 (17 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 2997 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3078 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 3126 seeds are put forward Round 1: 240 peptides, 31 chains. Longest chain 19 peptides. Score 0.612 Round 2: 257 peptides, 30 chains. Longest chain 20 peptides. Score 0.669 Round 3: 265 peptides, 27 chains. Longest chain 21 peptides. Score 0.719 Round 4: 268 peptides, 26 chains. Longest chain 24 peptides. Score 0.735 Round 5: 263 peptides, 28 chains. Longest chain 22 peptides. Score 0.705 Taking the results from Round 4 Chains 26, Residues 242, Estimated correctness of the model 72.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6785 restraints for refining 3044 atoms. 5843 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2323 (Rfree = 0.000) for 3044 atoms. Found 8 (16 requested) and removed 16 (13 requested) atoms. Cycle 22: After refmac, R = 0.2241 (Rfree = 0.000) for 3035 atoms. Found 3 (16 requested) and removed 13 (13 requested) atoms. Cycle 23: After refmac, R = 0.2227 (Rfree = 0.000) for 3024 atoms. Found 1 (15 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2200 (Rfree = 0.000) for 3012 atoms. Found 2 (15 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2172 (Rfree = 0.000) for 3001 atoms. Found 2 (14 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3084 seeds are put forward Round 1: 257 peptides, 33 chains. Longest chain 20 peptides. Score 0.634 Round 2: 279 peptides, 30 chains. Longest chain 35 peptides. Score 0.719 Round 3: 271 peptides, 31 chains. Longest chain 32 peptides. Score 0.691 Round 4: 268 peptides, 31 chains. Longest chain 33 peptides. Score 0.684 Round 5: 271 peptides, 32 chains. Longest chain 23 peptides. Score 0.681 Taking the results from Round 2 Chains 33, Residues 249, Estimated correctness of the model 69.1 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 33 chains (249 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6050 restraints for refining 3053 atoms. 4840 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2346 (Rfree = 0.000) for 3053 atoms. Found 12 (13 requested) and removed 27 (13 requested) atoms. Cycle 27: After refmac, R = 0.2213 (Rfree = 0.000) for 3034 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.2159 (Rfree = 0.000) for 3025 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.2111 (Rfree = 0.000) for 3017 atoms. Found 5 (13 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2069 (Rfree = 0.000) for 3008 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3114 seeds are put forward Round 1: 233 peptides, 31 chains. Longest chain 15 peptides. Score 0.592 Round 2: 240 peptides, 25 chains. Longest chain 21 peptides. Score 0.684 Round 3: 256 peptides, 31 chains. Longest chain 20 peptides. Score 0.655 Round 4: 258 peptides, 28 chains. Longest chain 22 peptides. Score 0.693 Round 5: 262 peptides, 29 chains. Longest chain 21 peptides. Score 0.692 Taking the results from Round 4 Chains 31, Residues 230, Estimated correctness of the model 63.7 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6369 restraints for refining 3053 atoms. 5326 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2354 (Rfree = 0.000) for 3053 atoms. Found 11 (13 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.2254 (Rfree = 0.000) for 3044 atoms. Found 5 (13 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2217 (Rfree = 0.000) for 3032 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.2186 (Rfree = 0.000) for 3022 atoms. Found 4 (13 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2156 (Rfree = 0.000) for 3013 atoms. Found 2 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 3074 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3094 seeds are put forward Round 1: 233 peptides, 32 chains. Longest chain 18 peptides. Score 0.578 Round 2: 254 peptides, 30 chains. Longest chain 20 peptides. Score 0.661 Round 3: 234 peptides, 31 chains. Longest chain 19 peptides. Score 0.594 Round 4: 243 peptides, 27 chains. Longest chain 29 peptides. Score 0.668 Round 5: 235 peptides, 30 chains. Longest chain 17 peptides. Score 0.610 Taking the results from Round 4 Chains 29, Residues 216, Estimated correctness of the model 58.1 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6651 restraints for refining 3053 atoms. 5722 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2366 (Rfree = 0.000) for 3053 atoms. Found 13 (13 requested) and removed 17 (13 requested) atoms. Cycle 37: After refmac, R = 0.2238 (Rfree = 0.000) for 3047 atoms. Found 4 (13 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2190 (Rfree = 0.000) for 3038 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2155 (Rfree = 0.000) for 3027 atoms. Found 1 (13 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 3013 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3075 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3093 seeds are put forward Round 1: 188 peptides, 32 chains. Longest chain 13 peptides. Score 0.425 Round 2: 224 peptides, 30 chains. Longest chain 21 peptides. Score 0.578 Round 3: 239 peptides, 30 chains. Longest chain 25 peptides. Score 0.622 Round 4: 246 peptides, 30 chains. Longest chain 22 peptides. Score 0.641 Round 5: 253 peptides, 29 chains. Longest chain 20 peptides. Score 0.670 Taking the results from Round 5 Chains 30, Residues 224, Estimated correctness of the model 58.5 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7113 reflections ( 99.69 % complete ) and 6632 restraints for refining 3053 atoms. 5668 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2306 (Rfree = 0.000) for 3053 atoms. Found 13 (13 requested) and removed 19 (13 requested) atoms. Cycle 42: After refmac, R = 0.2184 (Rfree = 0.000) for 3045 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2141 (Rfree = 0.000) for 3037 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2096 (Rfree = 0.000) for 3028 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2049 (Rfree = 0.000) for 3020 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.55 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3108 seeds are put forward Round 1: 199 peptides, 29 chains. Longest chain 20 peptides. Score 0.511 Round 2: 222 peptides, 28 chains. Longest chain 26 peptides. Score 0.599 Round 3: 227 peptides, 27 chains. Longest chain 26 peptides. Score 0.626 Round 4: 222 peptides, 29 chains. Longest chain 17 peptides. Score 0.585 Round 5: 215 peptides, 27 chains. Longest chain 20 peptides. Score 0.591 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 200, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7113 reflections ( 99.69 % complete ) and 6874 restraints for refining 3052 atoms. 6101 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2157 (Rfree = 0.000) for 3052 atoms. Found 0 (13 requested) and removed 11 (13 requested) atoms. Cycle 47: After refmac, R = 0.2116 (Rfree = 0.000) for 3039 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Cycle 48: After refmac, R = 0.2103 (Rfree = 0.000) for 3037 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Cycle 49: After refmac, R = 0.2097 (Rfree = 0.000) for 3035 atoms. Found 0 (13 requested) and removed 1 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:36:55 GMT 2018 Job finished. TimeTaking 42.74 Used memory is bytes: 5143672