Mon 24 Dec 00:50:01 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 1vk8-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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/1vk8-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 ============================================================ Mon 24 Dec 00:50:05 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/1vk8-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 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-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: 1vk8-3.2-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 3.200 Wilson plot Bfac: 50.12 5809 reflections ( 96.00 % complete ) and 0 restraints for refining 3743 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.2948 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2145 (Rfree = 0.000) for 3743 atoms. Found 16 (33 requested) and removed 40 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.92 3.39 Search for helices and strands: 0 residues in 0 chains, 3786 seeds are put forward NCS extension: 0 residues added, 3786 seeds are put forward Round 1: 185 peptides, 33 chains. Longest chain 14 peptides. Score 0.409 Round 2: 231 peptides, 34 chains. Longest chain 29 peptides. Score 0.564 Round 3: 254 peptides, 32 chains. Longest chain 28 peptides. Score 0.659 Round 4: 256 peptides, 29 chains. Longest chain 28 peptides. Score 0.699 Round 5: 253 peptides, 27 chains. Longest chain 27 peptides. Score 0.714 Taking the results from Round 5 Chains 29, Residues 226, Estimated correctness of the model 68.1 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 29 chains (226 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6308 restraints for refining 3096 atoms. 5245 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2219 (Rfree = 0.000) for 3096 atoms. Found 19 (27 requested) and removed 31 (13 requested) atoms. Cycle 2: After refmac, R = 0.2005 (Rfree = 0.000) for 3046 atoms. Found 13 (26 requested) and removed 25 (13 requested) atoms. Cycle 3: After refmac, R = 0.1877 (Rfree = 0.000) for 3015 atoms. Found 11 (26 requested) and removed 13 (13 requested) atoms. Cycle 4: After refmac, R = 0.1809 (Rfree = 0.000) for 3003 atoms. Found 6 (25 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.1776 (Rfree = 0.000) for 2993 atoms. Found 5 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 3.44 Search for helices and strands: 0 residues in 0 chains, 3103 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 3124 seeds are put forward Round 1: 234 peptides, 31 chains. Longest chain 19 peptides. Score 0.615 Round 2: 246 peptides, 28 chains. Longest chain 18 peptides. Score 0.685 Round 3: 248 peptides, 27 chains. Longest chain 21 peptides. Score 0.702 Round 4: 256 peptides, 29 chains. Longest chain 24 peptides. Score 0.699 Round 5: 232 peptides, 26 chains. Longest chain 26 peptides. Score 0.673 Taking the results from Round 3 Chains 29, Residues 221, Estimated correctness of the model 65.6 % 2 chains (30 residues) have been docked in sequence Building loops using Loopy2018 29 chains (221 residues) following loop building 2 chains (30 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6384 restraints for refining 3039 atoms. 5397 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2068 (Rfree = 0.000) for 3039 atoms. Found 19 (24 requested) and removed 20 (13 requested) atoms. Cycle 7: After refmac, R = 0.1910 (Rfree = 0.000) for 3032 atoms. Found 10 (24 requested) and removed 18 (13 requested) atoms. Cycle 8: After refmac, R = 0.1893 (Rfree = 0.000) for 3015 atoms. Found 8 (23 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.1905 (Rfree = 0.000) for 3005 atoms. Found 3 (23 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.1837 (Rfree = 0.000) for 2989 atoms. Found 6 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 3.47 Search for helices and strands: 0 residues in 0 chains, 3086 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 3120 seeds are put forward Round 1: 228 peptides, 32 chains. Longest chain 17 peptides. Score 0.582 Round 2: 259 peptides, 29 chains. Longest chain 20 peptides. Score 0.706 Round 3: 274 peptides, 30 chains. Longest chain 16 peptides. Score 0.730 Round 4: 258 peptides, 26 chains. Longest chain 28 peptides. Score 0.735 Round 5: 262 peptides, 29 chains. Longest chain 21 peptides. Score 0.713 Taking the results from Round 4 Chains 30, Residues 232, Estimated correctness of the model 72.3 % 5 chains (62 residues) have been docked in sequence Building loops using Loopy2018 30 chains (232 residues) following loop building 5 chains (62 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6211 restraints for refining 3096 atoms. 5062 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2000 (Rfree = 0.000) for 3096 atoms. Found 19 (22 requested) and removed 20 (13 requested) atoms. Cycle 12: After refmac, R = 0.1833 (Rfree = 0.000) for 3085 atoms. Found 12 (21 requested) and removed 15 (13 requested) atoms. Cycle 13: After refmac, R = 0.1761 (Rfree = 0.000) for 3074 atoms. Found 8 (21 requested) and removed 14 (13 requested) atoms. Cycle 14: After refmac, R = 0.1735 (Rfree = 0.000) for 3067 atoms. Found 2 (20 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.1750 (Rfree = 0.000) for 3053 atoms. Found 4 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 3.44 Search for helices and strands: 0 residues in 0 chains, 3142 seeds are put forward NCS extension: 20 residues added (15 deleted due to clashes), 3162 seeds are put forward Round 1: 221 peptides, 30 chains. Longest chain 24 peptides. Score 0.588 Round 2: 250 peptides, 29 chains. Longest chain 21 peptides. Score 0.684 Round 3: 251 peptides, 26 chains. Longest chain 27 peptides. Score 0.720 Round 4: 240 peptides, 30 chains. Longest chain 27 peptides. Score 0.645 Round 5: 226 peptides, 26 chains. Longest chain 23 peptides. Score 0.657 Taking the results from Round 3 Chains 28, Residues 225, Estimated correctness of the model 69.3 % 4 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 B and 71 B 26 chains (233 residues) following loop building 3 chains (96 residues) in sequence following loop building ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 5759 restraints for refining 3096 atoms. 4451 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2109 (Rfree = 0.000) for 3096 atoms. Found 16 (19 requested) and removed 39 (13 requested) atoms. Cycle 17: After refmac, R = 0.1893 (Rfree = 0.000) for 3056 atoms. Found 11 (18 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.1732 (Rfree = 0.000) for 3045 atoms. Found 7 (18 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.1671 (Rfree = 0.000) for 3031 atoms. Found 9 (17 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.1610 (Rfree = 0.000) for 3025 atoms. Found 4 (17 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 58 residues added (32 deleted due to clashes), 3164 seeds are put forward Round 1: 197 peptides, 30 chains. Longest chain 20 peptides. Score 0.506 Round 2: 231 peptides, 33 chains. Longest chain 17 peptides. Score 0.578 Round 3: 244 peptides, 30 chains. Longest chain 22 peptides. Score 0.656 Round 4: 230 peptides, 32 chains. Longest chain 15 peptides. Score 0.589 Round 5: 222 peptides, 28 chains. Longest chain 17 peptides. Score 0.619 Taking the results from Round 3 Chains 30, Residues 214, Estimated correctness of the model 55.3 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6792 restraints for refining 3087 atoms. 5882 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1892 (Rfree = 0.000) for 3087 atoms. Found 16 (16 requested) and removed 20 (13 requested) atoms. Cycle 22: After refmac, R = 0.1717 (Rfree = 0.000) for 3078 atoms. Found 10 (16 requested) and removed 13 (13 requested) atoms. Cycle 23: After refmac, R = 0.1664 (Rfree = 0.000) for 3072 atoms. Found 6 (16 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.1615 (Rfree = 0.000) for 3064 atoms. Found 0 (16 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1597 (Rfree = 0.000) for 3051 atoms. Found 3 (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, 3138 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 3149 seeds are put forward Round 1: 211 peptides, 34 chains. Longest chain 11 peptides. Score 0.494 Round 2: 228 peptides, 30 chains. Longest chain 21 peptides. Score 0.610 Round 3: 229 peptides, 33 chains. Longest chain 19 peptides. Score 0.572 Round 4: 234 peptides, 30 chains. Longest chain 20 peptides. Score 0.628 Round 5: 233 peptides, 33 chains. Longest chain 21 peptides. Score 0.584 Taking the results from Round 4 Chains 32, Residues 204, Estimated correctness of the model 48.4 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6548 restraints for refining 3080 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1813 (Rfree = 0.000) for 3080 atoms. Found 16 (16 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1625 (Rfree = 0.000) for 3070 atoms. Found 9 (16 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.1550 (Rfree = 0.000) for 3057 atoms. Found 11 (16 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.1485 (Rfree = 0.000) for 3054 atoms. Found 7 (16 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1419 (Rfree = 0.000) for 3047 atoms. Found 5 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 3142 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 3157 seeds are put forward Round 1: 203 peptides, 32 chains. Longest chain 14 peptides. Score 0.496 Round 2: 221 peptides, 28 chains. Longest chain 21 peptides. Score 0.616 Round 3: 242 peptides, 32 chains. Longest chain 26 peptides. Score 0.625 Round 4: 233 peptides, 30 chains. Longest chain 22 peptides. Score 0.625 Round 5: 227 peptides, 29 chains. Longest chain 23 peptides. Score 0.620 Taking the results from Round 4 Chains 30, Residues 203, Estimated correctness of the model 47.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6982 restraints for refining 3096 atoms. 6181 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1713 (Rfree = 0.000) for 3096 atoms. Found 16 (16 requested) and removed 16 (13 requested) atoms. Cycle 32: After refmac, R = 0.1587 (Rfree = 0.000) for 3091 atoms. Found 9 (16 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.1506 (Rfree = 0.000) for 3085 atoms. Found 7 (16 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1458 (Rfree = 0.000) for 3077 atoms. Found 9 (16 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1408 (Rfree = 0.000) for 3073 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3177 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 15 peptides. Score 0.383 Round 2: 219 peptides, 33 chains. Longest chain 15 peptides. Score 0.538 Round 3: 210 peptides, 33 chains. Longest chain 22 peptides. Score 0.506 Round 4: 222 peptides, 32 chains. Longest chain 20 peptides. Score 0.563 Round 5: 236 peptides, 33 chains. Longest chain 21 peptides. Score 0.594 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 7073 restraints for refining 3096 atoms. 6294 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1735 (Rfree = 0.000) for 3096 atoms. Found 14 (16 requested) and removed 14 (13 requested) atoms. Cycle 37: After refmac, R = 0.1608 (Rfree = 0.000) for 3093 atoms. Found 5 (16 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.1556 (Rfree = 0.000) for 3084 atoms. Found 2 (16 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1528 (Rfree = 0.000) for 3072 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1503 (Rfree = 0.000) for 3062 atoms. Found 4 (16 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 3162 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3184 seeds are put forward Round 1: 170 peptides, 29 chains. Longest chain 13 peptides. Score 0.418 Round 2: 208 peptides, 29 chains. Longest chain 15 peptides. Score 0.560 Round 3: 216 peptides, 30 chains. Longest chain 18 peptides. Score 0.572 Round 4: 216 peptides, 31 chains. Longest chain 22 peptides. Score 0.558 Round 5: 214 peptides, 27 chains. Longest chain 25 peptides. Score 0.608 Taking the results from Round 5 Chains 27, Residues 187, Estimated correctness of the model 43.2 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6872 restraints for refining 3096 atoms. 6055 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1675 (Rfree = 0.000) for 3096 atoms. Found 12 (16 requested) and removed 17 (13 requested) atoms. Cycle 42: After refmac, R = 0.1511 (Rfree = 0.000) for 3086 atoms. Found 8 (16 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.1456 (Rfree = 0.000) for 3079 atoms. Found 4 (16 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1423 (Rfree = 0.000) for 3068 atoms. Found 3 (16 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1350 (Rfree = 0.000) for 3055 atoms. Found 6 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 3156 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3173 seeds are put forward Round 1: 182 peptides, 30 chains. Longest chain 15 peptides. Score 0.449 Round 2: 187 peptides, 27 chains. Longest chain 19 peptides. Score 0.518 Round 3: 196 peptides, 26 chains. Longest chain 15 peptides. Score 0.565 Round 4: 204 peptides, 30 chains. Longest chain 22 peptides. Score 0.531 Round 5: 202 peptides, 33 chains. Longest chain 14 peptides. Score 0.476 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 170, Estimated correctness of the model 31.3 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 6 % 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 6993 restraints for refining 3085 atoms. 6298 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1569 (Rfree = 0.000) for 3085 atoms. Found 0 (16 requested) and removed 7 (13 requested) atoms. Cycle 47: After refmac, R = 0.1517 (Rfree = 0.000) for 3075 atoms. Found 0 (16 requested) and removed 3 (13 requested) atoms. Cycle 48: After refmac, R = 0.1506 (Rfree = 0.000) for 3071 atoms. Found 0 (16 requested) and removed 3 (13 requested) atoms. Cycle 49: After refmac, R = 0.1488 (Rfree = 0.000) for 3068 atoms. Found 0 (16 requested) and removed 1 (13 requested) atoms. Writing output files ... TimeTaking 36.45