Sun 23 Dec 23:52:12 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 1vk8-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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/1vk8-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 23:52:17 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/1vk8-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 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-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.4-parrot-mrncs.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 3749 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2961 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2526 (Rfree = 0.000) for 3749 atoms. Found 28 (28 requested) and removed 54 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.61 Search for helices and strands: 0 residues in 0 chains, 3806 seeds are put forward NCS extension: 0 residues added, 3806 seeds are put forward Round 1: 148 peptides, 30 chains. Longest chain 12 peptides. Score 0.303 Round 2: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.423 Round 3: 209 peptides, 33 chains. Longest chain 20 peptides. Score 0.502 Round 4: 222 peptides, 33 chains. Longest chain 14 peptides. Score 0.548 Round 5: 232 peptides, 31 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 5 Chains 32, Residues 201, Estimated correctness of the model 31.6 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6626 restraints for refining 3082 atoms. 5688 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1982 (Rfree = 0.000) for 3082 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 2: After refmac, R = 0.1743 (Rfree = 0.000) for 3029 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 3: After refmac, R = 0.1658 (Rfree = 0.000) for 3007 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.1588 (Rfree = 0.000) for 2990 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. Cycle 5: After refmac, R = 0.1552 (Rfree = 0.000) for 2970 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.61 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward NCS extension: 8 residues added (12 deleted due to clashes), 3102 seeds are put forward Round 1: 192 peptides, 31 chains. Longest chain 19 peptides. Score 0.471 Round 2: 221 peptides, 28 chains. Longest chain 19 peptides. Score 0.616 Round 3: 211 peptides, 28 chains. Longest chain 18 peptides. Score 0.585 Round 4: 227 peptides, 26 chains. Longest chain 25 peptides. Score 0.659 Round 5: 226 peptides, 28 chains. Longest chain 25 peptides. Score 0.631 Taking the results from Round 4 Chains 30, Residues 201, Estimated correctness of the model 46.7 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6225 restraints for refining 3027 atoms. 5213 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1988 (Rfree = 0.000) for 3027 atoms. Found 21 (22 requested) and removed 33 (11 requested) atoms. Cycle 7: After refmac, R = 0.1856 (Rfree = 0.000) for 3002 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.1813 (Rfree = 0.000) for 2992 atoms. Found 10 (22 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.1825 (Rfree = 0.000) for 2978 atoms. Found 14 (22 requested) and removed 19 (11 requested) atoms. Cycle 10: After refmac, R = 0.1827 (Rfree = 0.000) for 2965 atoms. Found 16 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 3077 seeds are put forward Round 1: 200 peptides, 34 chains. Longest chain 15 peptides. Score 0.452 Round 2: 216 peptides, 30 chains. Longest chain 24 peptides. Score 0.572 Round 3: 232 peptides, 32 chains. Longest chain 27 peptides. Score 0.595 Round 4: 225 peptides, 30 chains. Longest chain 28 peptides. Score 0.601 Round 5: 214 peptides, 28 chains. Longest chain 23 peptides. Score 0.594 Taking the results from Round 4 Chains 30, Residues 195, Estimated correctness of the model 29.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6944 restraints for refining 3044 atoms. 6194 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1942 (Rfree = 0.000) for 3044 atoms. Found 18 (22 requested) and removed 25 (11 requested) atoms. Cycle 12: After refmac, R = 0.1727 (Rfree = 0.000) for 3024 atoms. Found 6 (22 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.1706 (Rfree = 0.000) for 3005 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.1632 (Rfree = 0.000) for 2995 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.1600 (Rfree = 0.000) for 2984 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.69 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 3127 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 15 peptides. Score 0.358 Round 2: 187 peptides, 30 chains. Longest chain 19 peptides. Score 0.469 Round 3: 198 peptides, 29 chains. Longest chain 23 peptides. Score 0.526 Round 4: 193 peptides, 29 chains. Longest chain 17 peptides. Score 0.508 Round 5: 197 peptides, 25 chains. Longest chain 33 peptides. Score 0.583 Taking the results from Round 5 Chains 25, Residues 172, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7196 restraints for refining 3039 atoms. 6533 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1793 (Rfree = 0.000) for 3039 atoms. Found 19 (22 requested) and removed 25 (11 requested) atoms. Cycle 17: After refmac, R = 0.1729 (Rfree = 0.000) for 3030 atoms. Found 8 (22 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.1707 (Rfree = 0.000) for 3015 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.1363 (Rfree = 0.000) for 3005 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.1406 (Rfree = 0.000) for 2993 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 3082 seeds are put forward NCS extension: 39 residues added (8 deleted due to clashes), 3121 seeds are put forward Round 1: 161 peptides, 32 chains. Longest chain 11 peptides. Score 0.324 Round 2: 176 peptides, 27 chains. Longest chain 20 peptides. Score 0.477 Round 3: 178 peptides, 29 chains. Longest chain 15 peptides. Score 0.450 Round 4: 194 peptides, 29 chains. Longest chain 18 peptides. Score 0.511 Round 5: 191 peptides, 26 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 26, Residues 165, Estimated correctness of the model 10.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7173 restraints for refining 3042 atoms. 6539 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1706 (Rfree = 0.000) for 3042 atoms. Found 16 (22 requested) and removed 24 (11 requested) atoms. Cycle 22: After refmac, R = 0.1668 (Rfree = 0.000) for 3024 atoms. Found 11 (22 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1702 (Rfree = 0.000) for 3020 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.1567 (Rfree = 0.000) for 3012 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. Cycle 25: After refmac, R = 0.1334 (Rfree = 0.000) for 2999 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3125 seeds are put forward Round 1: 168 peptides, 33 chains. Longest chain 9 peptides. Score 0.337 Round 2: 204 peptides, 30 chains. Longest chain 17 peptides. Score 0.531 Round 3: 198 peptides, 32 chains. Longest chain 17 peptides. Score 0.478 Round 4: 205 peptides, 28 chains. Longest chain 24 peptides. Score 0.565 Round 5: 197 peptides, 32 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 4 Chains 28, Residues 177, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7124 restraints for refining 3084 atoms. 6444 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1734 (Rfree = 0.000) for 3084 atoms. Found 6 (23 requested) and removed 19 (11 requested) atoms. Cycle 27: After refmac, R = 0.1532 (Rfree = 0.000) for 3063 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1572 (Rfree = 0.000) for 3050 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1457 (Rfree = 0.000) for 3039 atoms. Found 1 (22 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.1435 (Rfree = 0.000) for 3020 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 3096 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 3120 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 9 peptides. Score 0.323 Round 2: 166 peptides, 27 chains. Longest chain 15 peptides. Score 0.437 Round 3: 166 peptides, 27 chains. Longest chain 10 peptides. Score 0.437 Round 4: 170 peptides, 27 chains. Longest chain 13 peptides. Score 0.453 Round 5: 170 peptides, 26 chains. Longest chain 12 peptides. Score 0.470 Taking the results from Round 5 Chains 26, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7376 restraints for refining 3046 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1549 (Rfree = 0.000) for 3046 atoms. Found 11 (22 requested) and removed 19 (11 requested) atoms. Cycle 32: After refmac, R = 0.1551 (Rfree = 0.000) for 3032 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 33: After refmac, R = 0.1476 (Rfree = 0.000) for 3027 atoms. Found 5 (22 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1439 (Rfree = 0.000) for 3018 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1363 (Rfree = 0.000) for 3005 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 0 residues added, 3077 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 9 peptides. Score 0.311 Round 2: 151 peptides, 24 chains. Longest chain 18 peptides. Score 0.429 Round 3: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.437 Round 4: 144 peptides, 21 chains. Longest chain 16 peptides. Score 0.455 Round 5: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Chains 21, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7281 restraints for refining 3015 atoms. 6810 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1444 (Rfree = 0.000) for 3015 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. Cycle 37: After refmac, R = 0.1385 (Rfree = 0.000) for 2998 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1514 (Rfree = 0.000) for 2989 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1296 (Rfree = 0.000) for 2983 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1552 (Rfree = 0.000) for 2971 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 3050 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3068 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 11 peptides. Score 0.252 Round 2: 144 peptides, 27 chains. Longest chain 13 peptides. Score 0.343 Round 3: 152 peptides, 29 chains. Longest chain 14 peptides. Score 0.341 Round 4: 158 peptides, 27 chains. Longest chain 17 peptides. Score 0.404 Round 5: 151 peptides, 29 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 4 Chains 27, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7234 restraints for refining 3029 atoms. 6737 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1477 (Rfree = 0.000) for 3029 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.1380 (Rfree = 0.000) for 3022 atoms. Found 9 (22 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.2019 (Rfree = 0.000) for 3011 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1315 (Rfree = 0.000) for 3014 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.1084 (Rfree = 0.000) for 3012 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.64 Search for helices and strands: 0 residues in 0 chains, 3098 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3110 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 9 peptides. Score 0.237 Round 2: 114 peptides, 22 chains. Longest chain 9 peptides. Score 0.302 Round 3: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.372 Round 4: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.333 Round 5: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 105, 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 7288 restraints for refining 3020 atoms. 6889 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1424 (Rfree = 0.000) for 3020 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1328 (Rfree = 0.000) for 3007 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1181 (Rfree = 0.000) for 2996 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1193 (Rfree = 0.000) for 2985 atoms. TimeTaking 41.75