Mon 24 Dec 07:36:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl6-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-parrot-noncs ############### 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 07:37:00 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-parrot-noncs/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 1343 and 0 Target number of residues in the AU: 1343 Target solvent content: 0.6282 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.2-parrot-noncs.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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.85 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: 124.815 3.200 Wilson plot Bfac: 65.59 31643 reflections ( 99.89 % complete ) and 0 restraints for refining 13850 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3261 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3171 (Rfree = 0.000) for 13850 atoms. Found 124 (124 requested) and removed 129 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 14075 seeds are put forward NCS extension: 0 residues added, 14075 seeds are put forward Round 1: 696 peptides, 125 chains. Longest chain 21 peptides. Score 0.355 Round 2: 866 peptides, 130 chains. Longest chain 19 peptides. Score 0.475 Round 3: 877 peptides, 114 chains. Longest chain 34 peptides. Score 0.535 Round 4: 923 peptides, 112 chains. Longest chain 29 peptides. Score 0.572 Round 5: 960 peptides, 106 chains. Longest chain 36 peptides. Score 0.613 Taking the results from Round 5 Chains 109, Residues 854, Estimated correctness of the model 44.5 % 7 chains (112 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 23842 restraints for refining 11328 atoms. 20116 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2929 (Rfree = 0.000) for 11328 atoms. Found 101 (101 requested) and removed 102 (50 requested) atoms. Cycle 2: After refmac, R = 0.2521 (Rfree = 0.000) for 11073 atoms. Found 91 (101 requested) and removed 71 (50 requested) atoms. Cycle 3: After refmac, R = 0.2386 (Rfree = 0.000) for 10990 atoms. Found 44 (99 requested) and removed 64 (49 requested) atoms. Cycle 4: After refmac, R = 0.2318 (Rfree = 0.000) for 10905 atoms. Found 67 (98 requested) and removed 57 (49 requested) atoms. Cycle 5: After refmac, R = 0.2288 (Rfree = 0.000) for 10880 atoms. Found 62 (97 requested) and removed 55 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11337 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 11358 seeds are put forward Round 1: 937 peptides, 130 chains. Longest chain 25 peptides. Score 0.527 Round 2: 1003 peptides, 117 chains. Longest chain 51 peptides. Score 0.608 Round 3: 1007 peptides, 106 chains. Longest chain 51 peptides. Score 0.640 Round 4: 1008 peptides, 107 chains. Longest chain 35 peptides. Score 0.638 Round 5: 1026 peptides, 112 chains. Longest chain 38 peptides. Score 0.635 Taking the results from Round 3 Chains 114, Residues 901, Estimated correctness of the model 51.4 % 16 chains (239 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22560 restraints for refining 11334 atoms. 18191 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2591 (Rfree = 0.000) for 11334 atoms. Found 88 (101 requested) and removed 92 (50 requested) atoms. Cycle 7: After refmac, R = 0.2399 (Rfree = 0.000) for 11230 atoms. Found 47 (101 requested) and removed 64 (50 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 11163 atoms. Found 27 (100 requested) and removed 64 (50 requested) atoms. Cycle 9: After refmac, R = 0.2401 (Rfree = 0.000) for 11082 atoms. Found 42 (99 requested) and removed 77 (49 requested) atoms. Cycle 10: After refmac, R = 0.2397 (Rfree = 0.000) for 11019 atoms. Found 87 (99 requested) and removed 72 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11388 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 11407 seeds are put forward Round 1: 921 peptides, 117 chains. Longest chain 30 peptides. Score 0.556 Round 2: 999 peptides, 113 chains. Longest chain 35 peptides. Score 0.617 Round 3: 1020 peptides, 116 chains. Longest chain 34 peptides. Score 0.621 Round 4: 1013 peptides, 112 chains. Longest chain 39 peptides. Score 0.628 Round 5: 1025 peptides, 114 chains. Longest chain 46 peptides. Score 0.629 Taking the results from Round 5 Chains 121, Residues 911, Estimated correctness of the model 48.6 % 16 chains (218 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22626 restraints for refining 11334 atoms. 18301 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2692 (Rfree = 0.000) for 11334 atoms. Found 101 (101 requested) and removed 67 (50 requested) atoms. Cycle 12: After refmac, R = 0.2471 (Rfree = 0.000) for 11289 atoms. Found 66 (102 requested) and removed 77 (51 requested) atoms. Cycle 13: After refmac, R = 0.2393 (Rfree = 0.000) for 11225 atoms. Found 53 (101 requested) and removed 62 (50 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2336 (Rfree = 0.000) for 11188 atoms. Found 45 (100 requested) and removed 60 (50 requested) atoms. Cycle 15: After refmac, R = 0.2295 (Rfree = 0.000) for 11142 atoms. Found 42 (100 requested) and removed 61 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 11525 seeds are put forward NCS extension: 26 residues added (19 deleted due to clashes), 11551 seeds are put forward Round 1: 886 peptides, 130 chains. Longest chain 37 peptides. Score 0.490 Round 2: 969 peptides, 117 chains. Longest chain 35 peptides. Score 0.587 Round 3: 960 peptides, 110 chains. Longest chain 27 peptides. Score 0.602 Round 4: 997 peptides, 113 chains. Longest chain 35 peptides. Score 0.616 Round 5: 965 peptides, 108 chains. Longest chain 31 peptides. Score 0.610 Taking the results from Round 4 Chains 122, Residues 884, Estimated correctness of the model 45.3 % 19 chains (275 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22632 restraints for refining 11335 atoms. 18189 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2656 (Rfree = 0.000) for 11335 atoms. Found 79 (101 requested) and removed 82 (50 requested) atoms. Cycle 17: After refmac, R = 0.2498 (Rfree = 0.000) for 11269 atoms. Found 55 (101 requested) and removed 71 (50 requested) atoms. Cycle 18: After refmac, R = 0.2498 (Rfree = 0.000) for 11222 atoms. Found 56 (100 requested) and removed 65 (50 requested) atoms. Cycle 19: After refmac, R = 0.2369 (Rfree = 0.000) for 11182 atoms. Found 51 (100 requested) and removed 57 (50 requested) atoms. Cycle 20: After refmac, R = 0.2239 (Rfree = 0.000) for 11151 atoms. Found 28 (100 requested) and removed 60 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11497 seeds are put forward NCS extension: 22 residues added (10 deleted due to clashes), 11519 seeds are put forward Round 1: 871 peptides, 123 chains. Longest chain 34 peptides. Score 0.502 Round 2: 957 peptides, 110 chains. Longest chain 40 peptides. Score 0.600 Round 3: 959 peptides, 104 chains. Longest chain 42 peptides. Score 0.618 Round 4: 962 peptides, 110 chains. Longest chain 31 peptides. Score 0.603 Round 5: 973 peptides, 104 chains. Longest chain 33 peptides. Score 0.626 Taking the results from Round 5 Chains 111, Residues 869, Estimated correctness of the model 47.9 % 17 chains (278 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22273 restraints for refining 11332 atoms. 17848 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2602 (Rfree = 0.000) for 11332 atoms. Found 91 (101 requested) and removed 84 (50 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 11267 atoms. Found 65 (101 requested) and removed 65 (50 requested) atoms. Cycle 23: After refmac, R = 0.2405 (Rfree = 0.000) for 11216 atoms. Found 64 (101 requested) and removed 58 (50 requested) atoms. Cycle 24: After refmac, R = 0.2419 (Rfree = 0.000) for 11186 atoms. Found 87 (100 requested) and removed 60 (50 requested) atoms. Cycle 25: After refmac, R = 0.2351 (Rfree = 0.000) for 11184 atoms. Found 56 (100 requested) and removed 55 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11563 seeds are put forward NCS extension: 25 residues added (20 deleted due to clashes), 11588 seeds are put forward Round 1: 883 peptides, 127 chains. Longest chain 22 peptides. Score 0.498 Round 2: 975 peptides, 115 chains. Longest chain 34 peptides. Score 0.597 Round 3: 968 peptides, 118 chains. Longest chain 40 peptides. Score 0.584 Round 4: 961 peptides, 112 chains. Longest chain 34 peptides. Score 0.596 Round 5: 965 peptides, 109 chains. Longest chain 24 peptides. Score 0.607 Taking the results from Round 5 Chains 118, Residues 856, Estimated correctness of the model 42.9 % 16 chains (201 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 31643 reflections ( 99.89 % complete ) and 23467 restraints for refining 11334 atoms. 19424 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2625 (Rfree = 0.000) for 11334 atoms. Found 101 (101 requested) and removed 71 (50 requested) atoms. Cycle 27: After refmac, R = 0.2420 (Rfree = 0.000) for 11295 atoms. Found 51 (101 requested) and removed 67 (50 requested) atoms. Cycle 28: After refmac, R = 0.2294 (Rfree = 0.000) for 11233 atoms. Found 40 (101 requested) and removed 57 (50 requested) atoms. Cycle 29: After refmac, R = 0.2268 (Rfree = 0.000) for 11195 atoms. Found 49 (100 requested) and removed 52 (50 requested) atoms. Cycle 30: After refmac, R = 0.2231 (Rfree = 0.000) for 11169 atoms. Found 43 (100 requested) and removed 60 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.89 Search for helices and strands: 0 residues in 0 chains, 11555 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 11566 seeds are put forward Round 1: 856 peptides, 122 chains. Longest chain 25 peptides. Score 0.494 Round 2: 942 peptides, 118 chains. Longest chain 29 peptides. Score 0.567 Round 3: 949 peptides, 110 chains. Longest chain 39 peptides. Score 0.595 Round 4: 960 peptides, 111 chains. Longest chain 36 peptides. Score 0.599 Round 5: 938 peptides, 103 chains. Longest chain 32 peptides. Score 0.608 Taking the results from Round 5 Chains 107, Residues 835, Estimated correctness of the model 43.2 % 10 chains (174 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 31643 reflections ( 99.89 % complete ) and 23514 restraints for refining 11332 atoms. 19603 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2478 (Rfree = 0.000) for 11332 atoms. Found 101 (101 requested) and removed 66 (50 requested) atoms. Cycle 32: After refmac, R = 0.2301 (Rfree = 0.000) for 11320 atoms. Found 34 (102 requested) and removed 62 (51 requested) atoms. Cycle 33: After refmac, R = 0.2320 (Rfree = 0.000) for 11241 atoms. Found 53 (101 requested) and removed 56 (50 requested) atoms. Cycle 34: After refmac, R = 0.2506 (Rfree = 0.000) for 11211 atoms. Found 100 (100 requested) and removed 76 (50 requested) atoms. Cycle 35: After refmac, R = 0.2483 (Rfree = 0.000) for 11202 atoms. Found 100 (100 requested) and removed 64 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11612 seeds are put forward NCS extension: 14 residues added (15 deleted due to clashes), 11626 seeds are put forward Round 1: 754 peptides, 117 chains. Longest chain 23 peptides. Score 0.433 Round 2: 846 peptides, 109 chains. Longest chain 31 peptides. Score 0.529 Round 3: 869 peptides, 110 chains. Longest chain 34 peptides. Score 0.542 Round 4: 866 peptides, 100 chains. Longest chain 38 peptides. Score 0.571 Round 5: 860 peptides, 109 chains. Longest chain 38 peptides. Score 0.539 Taking the results from Round 4 Chains 103, Residues 766, Estimated correctness of the model 33.0 % 7 chains (102 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 24721 restraints for refining 11335 atoms. 21414 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2407 (Rfree = 0.000) for 11335 atoms. Found 101 (101 requested) and removed 60 (50 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2341 (Rfree = 0.000) for 11339 atoms. Found 65 (102 requested) and removed 61 (51 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 11318 atoms. Found 50 (101 requested) and removed 54 (50 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2138 (Rfree = 0.000) for 11285 atoms. Found 53 (101 requested) and removed 63 (50 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2133 (Rfree = 0.000) for 11251 atoms. Found 72 (101 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 11625 seeds are put forward NCS extension: 25 residues added (12 deleted due to clashes), 11650 seeds are put forward Round 1: 768 peptides, 121 chains. Longest chain 20 peptides. Score 0.430 Round 2: 847 peptides, 116 chains. Longest chain 27 peptides. Score 0.507 Round 3: 869 peptides, 108 chains. Longest chain 30 peptides. Score 0.548 Round 4: 882 peptides, 110 chains. Longest chain 28 peptides. Score 0.551 Round 5: 877 peptides, 114 chains. Longest chain 31 peptides. Score 0.535 Taking the results from Round 4 Chains 119, Residues 772, Estimated correctness of the model 27.2 % 12 chains (110 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 24539 restraints for refining 11333 atoms. 21198 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2318 (Rfree = 0.000) for 11333 atoms. Found 85 (101 requested) and removed 61 (50 requested) atoms. Cycle 42: After refmac, R = 0.2273 (Rfree = 0.000) for 11311 atoms. Found 71 (101 requested) and removed 54 (50 requested) atoms. Cycle 43: After refmac, R = 0.2225 (Rfree = 0.000) for 11294 atoms. Found 61 (101 requested) and removed 53 (50 requested) atoms. Cycle 44: After refmac, R = 0.2148 (Rfree = 0.000) for 11268 atoms. Found 53 (101 requested) and removed 54 (50 requested) atoms. Cycle 45: After refmac, R = 0.2135 (Rfree = 0.000) for 11245 atoms. Found 49 (101 requested) and removed 54 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11616 seeds are put forward NCS extension: 9 residues added (12 deleted due to clashes), 11625 seeds are put forward Round 1: 752 peptides, 124 chains. Longest chain 15 peptides. Score 0.406 Round 2: 844 peptides, 102 chains. Longest chain 32 peptides. Score 0.550 Round 3: 831 peptides, 106 chains. Longest chain 27 peptides. Score 0.528 Round 4: 841 peptides, 102 chains. Longest chain 35 peptides. Score 0.548 Round 5: 857 peptides, 104 chains. Longest chain 36 peptides. Score 0.553 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 113, Residues 753, Estimated correctness of the model 27.8 % 11 chains (106 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 113 chains (753 residues) following loop building 11 chains (106 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31643 reflections ( 99.89 % complete ) and 24752 restraints for refining 11333 atoms. 21484 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2410 (Rfree = 0.000) for 11333 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 11240 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 48: After refmac, R = 0.2241 (Rfree = 0.000) for 11168 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 49: After refmac, R = 0.2232 (Rfree = 0.000) for 11100 atoms. TimeTaking 141.12