Sun 23 Dec 22:23:10 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 1vk8-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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/1vk8-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 22:23:19 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/1vk8-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 278 and 0 Target number of residues in the AU: 278 Target solvent content: 0.6028 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: 1vk8-3.4-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: 1vk8-3.4-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 3.400 Wilson plot Bfac: 53.37 4829 reflections ( 96.04 % complete ) and 0 restraints for refining 3753 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2998 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2584 (Rfree = 0.000) for 3753 atoms. Found 27 (28 requested) and removed 61 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 3813 seeds are put forward NCS extension: 0 residues added, 3813 seeds are put forward Round 1: 147 peptides, 25 chains. Longest chain 13 peptides. Score 0.394 Round 2: 189 peptides, 29 chains. Longest chain 13 peptides. Score 0.493 Round 3: 193 peptides, 28 chains. Longest chain 22 peptides. Score 0.523 Round 4: 205 peptides, 30 chains. Longest chain 22 peptides. Score 0.535 Round 5: 204 peptides, 28 chains. Longest chain 18 peptides. Score 0.562 Taking the results from Round 5 Chains 28, Residues 176, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7133 restraints for refining 3084 atoms. 6457 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2003 (Rfree = 0.000) for 3084 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 2: After refmac, R = 0.1726 (Rfree = 0.000) for 3042 atoms. Found 12 (23 requested) and removed 18 (11 requested) atoms. Cycle 3: After refmac, R = 0.1574 (Rfree = 0.000) for 3030 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.1525 (Rfree = 0.000) for 3013 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.1472 (Rfree = 0.000) for 2999 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3137 seeds are put forward Round 1: 184 peptides, 35 chains. Longest chain 16 peptides. Score 0.370 Round 2: 222 peptides, 37 chains. Longest chain 12 peptides. Score 0.487 Round 3: 227 peptides, 35 chains. Longest chain 15 peptides. Score 0.536 Round 4: 234 peptides, 37 chains. Longest chain 18 peptides. Score 0.530 Round 5: 240 peptides, 35 chains. Longest chain 18 peptides. Score 0.579 Taking the results from Round 5 Chains 35, Residues 205, Estimated correctness of the model 21.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6717 restraints for refining 2982 atoms. 5932 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1927 (Rfree = 0.000) for 2982 atoms. Found 15 (22 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.1799 (Rfree = 0.000) for 2967 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.1805 (Rfree = 0.000) for 2950 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.1742 (Rfree = 0.000) for 2942 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.1682 (Rfree = 0.000) for 2933 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3072 seeds are put forward Round 1: 205 peptides, 33 chains. Longest chain 16 peptides. Score 0.488 Round 2: 194 peptides, 28 chains. Longest chain 22 peptides. Score 0.527 Round 3: 201 peptides, 28 chains. Longest chain 23 peptides. Score 0.552 Round 4: 221 peptides, 28 chains. Longest chain 23 peptides. Score 0.616 Round 5: 223 peptides, 30 chains. Longest chain 16 peptides. Score 0.595 Taking the results from Round 4 Chains 28, Residues 193, Estimated correctness of the model 33.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6850 restraints for refining 2998 atoms. 6106 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1764 (Rfree = 0.000) for 2998 atoms. Found 11 (22 requested) and removed 19 (11 requested) atoms. Cycle 12: After refmac, R = 0.1588 (Rfree = 0.000) for 2987 atoms. Found 6 (22 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.1581 (Rfree = 0.000) for 2971 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.1539 (Rfree = 0.000) for 2962 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.1535 (Rfree = 0.000) for 2951 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 3046 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3065 seeds are put forward Round 1: 189 peptides, 35 chains. Longest chain 12 peptides. Score 0.391 Round 2: 223 peptides, 35 chains. Longest chain 14 peptides. Score 0.522 Round 3: 239 peptides, 34 chains. Longest chain 19 peptides. Score 0.590 Round 4: 243 peptides, 32 chains. Longest chain 27 peptides. Score 0.628 Round 5: 250 peptides, 35 chains. Longest chain 19 peptides. Score 0.610 Taking the results from Round 4 Chains 32, Residues 211, Estimated correctness of the model 37.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7161 restraints for refining 3081 atoms. 6349 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1838 (Rfree = 0.000) for 3081 atoms. Found 9 (23 requested) and removed 26 (11 requested) atoms. Cycle 17: After refmac, R = 0.1634 (Rfree = 0.000) for 3054 atoms. Found 4 (23 requested) and removed 19 (11 requested) atoms. Cycle 18: After refmac, R = 0.1577 (Rfree = 0.000) for 3036 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.1492 (Rfree = 0.000) for 3026 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.1477 (Rfree = 0.000) for 3014 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.64 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward NCS extension: 28 residues added (14 deleted due to clashes), 3144 seeds are put forward Round 1: 180 peptides, 33 chains. Longest chain 26 peptides. Score 0.389 Round 2: 216 peptides, 32 chains. Longest chain 28 peptides. Score 0.543 Round 3: 216 peptides, 31 chains. Longest chain 28 peptides. Score 0.558 Round 4: 222 peptides, 35 chains. Longest chain 13 peptides. Score 0.518 Round 5: 217 peptides, 36 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 3 Chains 31, Residues 185, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7218 restraints for refining 3068 atoms. 6509 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1555 (Rfree = 0.000) for 3068 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 22: After refmac, R = 0.1399 (Rfree = 0.000) for 3047 atoms. Found 4 (23 requested) and removed 16 (11 requested) atoms. Cycle 23: After refmac, R = 0.1442 (Rfree = 0.000) for 3033 atoms. Found 2 (22 requested) and removed 16 (11 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 3018 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 25: After refmac, R = 0.1320 (Rfree = 0.000) for 3014 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 3118 seeds are put forward NCS extension: 52 residues added (0 deleted due to clashes), 3170 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 8 peptides. Score 0.303 Round 2: 182 peptides, 32 chains. Longest chain 17 peptides. Score 0.414 Round 3: 173 peptides, 30 chains. Longest chain 15 peptides. Score 0.413 Round 4: 168 peptides, 25 chains. Longest chain 17 peptides. Score 0.480 Round 5: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 4 Chains 25, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7351 restraints for refining 3066 atoms. 6804 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1492 (Rfree = 0.000) for 3066 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.1351 (Rfree = 0.000) for 3058 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1582 (Rfree = 0.000) for 3051 atoms. Found 11 (23 requested) and removed 21 (11 requested) atoms. Cycle 29: After refmac, R = 0.1313 (Rfree = 0.000) for 3038 atoms. Found 2 (22 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.1371 (Rfree = 0.000) for 3021 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 3.64 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3136 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.302 Round 2: 170 peptides, 29 chains. Longest chain 13 peptides. Score 0.418 Round 3: 177 peptides, 32 chains. Longest chain 12 peptides. Score 0.394 Round 4: 161 peptides, 28 chains. Longest chain 9 peptides. Score 0.398 Round 5: 174 peptides, 31 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 2 Chains 29, Residues 141, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7247 restraints for refining 3070 atoms. 6695 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1394 (Rfree = 0.000) for 3070 atoms. Found 7 (23 requested) and removed 24 (11 requested) atoms. Cycle 32: After refmac, R = 0.1341 (Rfree = 0.000) for 3050 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.1248 (Rfree = 0.000) for 3048 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1365 (Rfree = 0.000) for 3040 atoms. Found 12 (22 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1764 (Rfree = 0.000) for 3038 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.61 Search for helices and strands: 0 residues in 0 chains, 3166 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3180 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.253 Round 2: 134 peptides, 26 chains. Longest chain 11 peptides. Score 0.317 Round 3: 139 peptides, 24 chains. Longest chain 16 peptides. Score 0.378 Round 4: 141 peptides, 25 chains. Longest chain 12 peptides. Score 0.368 Round 5: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 5 Chains 25, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7406 restraints for refining 3084 atoms. 6943 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1375 (Rfree = 0.000) for 3084 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.1221 (Rfree = 0.000) for 3069 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.1070 (Rfree = 0.000) for 3053 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.1096 (Rfree = 0.000) for 3042 atoms. Found 1 (22 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1218 (Rfree = 0.000) for 3031 atoms. Found 9 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 3152 seeds are put forward NCS extension: 0 residues added, 3152 seeds are put forward Round 1: 143 peptides, 30 chains. Longest chain 10 peptides. Score 0.280 Round 2: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.390 Round 3: 163 peptides, 29 chains. Longest chain 14 peptides. Score 0.389 Round 4: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.397 Round 5: 164 peptides, 26 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 5 Chains 26, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7417 restraints for refining 3084 atoms. 6891 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1400 (Rfree = 0.000) for 3084 atoms. Found 8 (23 requested) and removed 15 (11 requested) atoms. Cycle 42: After refmac, R = 0.1321 (Rfree = 0.000) for 3072 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.1283 (Rfree = 0.000) for 3061 atoms. Found 4 (23 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.1309 (Rfree = 0.000) for 3048 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.1200 (Rfree = 0.000) for 3039 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3172 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 10 peptides. Score 0.278 Round 2: 149 peptides, 29 chains. Longest chain 11 peptides. Score 0.327 Round 3: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.378 Round 4: 143 peptides, 26 chains. Longest chain 8 peptides. Score 0.357 Round 5: 142 peptides, 27 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 125, 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 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4829 reflections ( 96.04 % complete ) and 7402 restraints for refining 3079 atoms. 6929 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1447 (Rfree = 0.000) for 3079 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1373 (Rfree = 0.000) for 3067 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 48: After refmac, R = 0.1376 (Rfree = 0.000) for 3055 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1331 (Rfree = 0.000) for 3044 atoms. TimeTaking 51.87