null Sun 23 Dec 22:22:49 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 1zyb-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-2.1-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/1zyb-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-2.1-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 22:22:59 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/1zyb-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-2.1-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 389 and 0 Target number of residues in the AU: 389 Target solvent content: 0.5468 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 464 Adjusted target solvent content: 0.46 Input MTZ file: 1zyb-2.1-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: 179 Cell parameters: 115.980 115.980 119.640 90.000 90.000 120.000 Input sequence file: 1zyb-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 3712 target number of atoms Had to go as low as 0.45 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 1 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: 100.441 2.100 Wilson plot Bfac: 34.47 28226 reflections ( 99.73 % complete ) and 0 restraints for refining 4091 atoms. Observations/parameters ratio is 1.72 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2966 (Rfree = 0.000) for 4091 atoms. Found 101 (121 requested) and removed 75 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.49 NCS extension: 0 residues added, 4117 seeds are put forward Round 1: 196 peptides, 14 chains. Longest chain 33 peptides. Score 0.666 Round 2: 217 peptides, 14 chains. Longest chain 45 peptides. Score 0.712 Round 3: 219 peptides, 7 chains. Longest chain 63 peptides. Score 0.784 Round 4: 223 peptides, 6 chains. Longest chain 76 peptides. Score 0.800 Round 5: 225 peptides, 5 chains. Longest chain 87 peptides. Score 0.811 Taking the results from Round 5 Chains 5, Residues 220, Estimated correctness of the model 96.1 % 3 chains (210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 B and 164 B 3 chains (224 residues) following loop building 2 chains (219 residues) in sequence following loop building ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 4273 restraints for refining 3352 atoms. 2430 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3073 (Rfree = 0.000) for 3352 atoms. Found 101 (101 requested) and removed 83 (50 requested) atoms. Cycle 2: After refmac, R = 0.2737 (Rfree = 0.000) for 3308 atoms. Found 98 (98 requested) and removed 59 (50 requested) atoms. Cycle 3: After refmac, R = 0.2544 (Rfree = 0.000) for 3274 atoms. Found 92 (95 requested) and removed 50 (49 requested) atoms. Cycle 4: After refmac, R = 0.2447 (Rfree = 0.000) for 3270 atoms. Found 92 (92 requested) and removed 51 (49 requested) atoms. Cycle 5: After refmac, R = 0.2385 (Rfree = 0.000) for 3282 atoms. Found 79 (90 requested) and removed 52 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.30 2.43 NCS extension: 0 residues added, 3312 seeds are put forward Round 1: 224 peptides, 4 chains. Longest chain 97 peptides. Score 0.819 Round 2: 222 peptides, 4 chains. Longest chain 105 peptides. Score 0.816 Round 3: 225 peptides, 6 chains. Longest chain 90 peptides. Score 0.803 Round 4: 223 peptides, 3 chains. Longest chain 105 peptides. Score 0.826 Round 5: 226 peptides, 3 chains. Longest chain 97 peptides. Score 0.830 Taking the results from Round 5 Chains 3, Residues 223, Estimated correctness of the model 96.8 % 3 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 188 B and 191 B 2 chains (225 residues) following loop building 2 chains (225 residues) in sequence following loop building ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 3211 restraints for refining 2999 atoms. 1331 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2562 (Rfree = 0.000) for 2999 atoms. Found 80 (80 requested) and removed 60 (44 requested) atoms. Cycle 7: After refmac, R = 0.2409 (Rfree = 0.000) for 3004 atoms. Found 78 (78 requested) and removed 45 (44 requested) atoms. Cycle 8: After refmac, R = 0.2335 (Rfree = 0.000) for 3019 atoms. Found 76 (77 requested) and removed 46 (45 requested) atoms. Cycle 9: After refmac, R = 0.2249 (Rfree = 0.000) for 3035 atoms. Found 76 (76 requested) and removed 48 (45 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 3035 atoms. Found 75 (75 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 3064 seeds are put forward Round 1: 224 peptides, 4 chains. Longest chain 97 peptides. Score 0.819 Round 2: 227 peptides, 2 chains. Longest chain 118 peptides. Score 0.839 Round 3: 224 peptides, 5 chains. Longest chain 74 peptides. Score 0.810 Round 4: 226 peptides, 4 chains. Longest chain 123 peptides. Score 0.821 Round 5: 222 peptides, 4 chains. Longest chain 100 peptides. Score 0.816 Taking the results from Round 2 Chains 3, Residues 225, Estimated correctness of the model 97.1 % 2 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 125 A 2 chains (227 residues) following loop building 1 chains (223 residues) in sequence following loop building ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2945 restraints for refining 2901 atoms. 1070 conditional restraints added. Observations/parameters ratio is 2.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2413 (Rfree = 0.000) for 2901 atoms. Found 69 (69 requested) and removed 47 (43 requested) atoms. Cycle 12: After refmac, R = 0.2281 (Rfree = 0.000) for 2907 atoms. Found 68 (68 requested) and removed 43 (43 requested) atoms. Cycle 13: After refmac, R = 0.2187 (Rfree = 0.000) for 2917 atoms. Found 66 (66 requested) and removed 43 (43 requested) atoms. Cycle 14: After refmac, R = 0.2148 (Rfree = 0.000) for 2923 atoms. Found 64 (64 requested) and removed 44 (43 requested) atoms. Cycle 15: After refmac, R = 0.2126 (Rfree = 0.000) for 2932 atoms. Found 63 (63 requested) and removed 44 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.28 2.41 NCS extension: 0 residues added, 2951 seeds are put forward Round 1: 226 peptides, 3 chains. Longest chain 105 peptides. Score 0.830 Round 2: 227 peptides, 1 chains. Longest chain 227 peptides. Score 0.847 Round 3: 226 peptides, 2 chains. Longest chain 141 peptides. Score 0.838 Round 4: 227 peptides, 2 chains. Longest chain 192 peptides. Score 0.839 Round 5: 226 peptides, 3 chains. Longest chain 114 peptides. Score 0.830 Taking the results from Round 2 Chains 1, Residues 226, Estimated correctness of the model 97.3 % 1 chains (226 residues) have been docked in sequence ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2758 restraints for refining 2824 atoms. 872 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2352 (Rfree = 0.000) for 2824 atoms. Found 59 (59 requested) and removed 48 (42 requested) atoms. Cycle 17: After refmac, R = 0.2203 (Rfree = 0.000) for 2825 atoms. Found 57 (57 requested) and removed 42 (42 requested) atoms. Cycle 18: After refmac, R = 0.2159 (Rfree = 0.000) for 2832 atoms. Found 55 (55 requested) and removed 42 (42 requested) atoms. Cycle 19: After refmac, R = 0.2137 (Rfree = 0.000) for 2838 atoms. Found 54 (54 requested) and removed 44 (42 requested) atoms. Cycle 20: After refmac, R = 0.2132 (Rfree = 0.000) for 2839 atoms. Found 52 (52 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2847 seeds are put forward Round 1: 227 peptides, 1 chains. Longest chain 227 peptides. Score 0.847 Round 2: 227 peptides, 2 chains. Longest chain 122 peptides. Score 0.839 Round 3: 227 peptides, 2 chains. Longest chain 142 peptides. Score 0.839 Round 4: 226 peptides, 4 chains. Longest chain 126 peptides. Score 0.821 Round 5: 225 peptides, 5 chains. Longest chain 95 peptides. Score 0.811 Taking the results from Round 1 Chains 1, Residues 226, Estimated correctness of the model 97.3 % 1 chains (226 residues) have been docked in sequence ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2680 restraints for refining 2759 atoms. 794 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2295 (Rfree = 0.000) for 2759 atoms. Found 49 (49 requested) and removed 45 (41 requested) atoms. Cycle 22: After refmac, R = 0.2160 (Rfree = 0.000) for 2758 atoms. Found 48 (48 requested) and removed 41 (41 requested) atoms. Cycle 23: After refmac, R = 0.2123 (Rfree = 0.000) for 2757 atoms. Found 46 (46 requested) and removed 42 (41 requested) atoms. Cycle 24: After refmac, R = 0.2093 (Rfree = 0.000) for 2752 atoms. Found 44 (44 requested) and removed 42 (41 requested) atoms. Cycle 25: After refmac, R = 0.2081 (Rfree = 0.000) for 2748 atoms. Found 43 (43 requested) and removed 44 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2747 seeds are put forward Round 1: 225 peptides, 2 chains. Longest chain 140 peptides. Score 0.836 Round 2: 227 peptides, 1 chains. Longest chain 227 peptides. Score 0.847 Round 3: 227 peptides, 1 chains. Longest chain 227 peptides. Score 0.847 Round 4: 225 peptides, 2 chains. Longest chain 177 peptides. Score 0.836 Round 5: 225 peptides, 4 chains. Longest chain 79 peptides. Score 0.820 Taking the results from Round 3 Chains 1, Residues 226, Estimated correctness of the model 97.3 % 1 chains (226 residues) have been docked in sequence ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2622 restraints for refining 2671 atoms. 736 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2261 (Rfree = 0.000) for 2671 atoms. Found 39 (39 requested) and removed 45 (39 requested) atoms. Cycle 27: After refmac, R = 0.2138 (Rfree = 0.000) for 2655 atoms. Found 39 (39 requested) and removed 39 (39 requested) atoms. Cycle 28: After refmac, R = 0.2089 (Rfree = 0.000) for 2650 atoms. Found 39 (39 requested) and removed 39 (39 requested) atoms. Cycle 29: After refmac, R = 0.2045 (Rfree = 0.000) for 2647 atoms. Found 39 (39 requested) and removed 25 (39 requested) atoms. Cycle 30: After refmac, R = 0.2029 (Rfree = 0.000) for 2654 atoms. Found 39 (39 requested) and removed 40 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2653 seeds are put forward Round 1: 225 peptides, 2 chains. Longest chain 140 peptides. Score 0.836 Round 2: 226 peptides, 2 chains. Longest chain 122 peptides. Score 0.838 Round 3: 227 peptides, 1 chains. Longest chain 227 peptides. Score 0.847 Round 4: 227 peptides, 2 chains. Longest chain 181 peptides. Score 0.839 Round 5: 225 peptides, 4 chains. Longest chain 101 peptides. Score 0.820 Taking the results from Round 3 Chains 1, Residues 226, Estimated correctness of the model 97.3 % 1 chains (226 residues) have been docked in sequence ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2515 restraints for refining 2594 atoms. 629 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2268 (Rfree = 0.000) for 2594 atoms. Found 38 (38 requested) and removed 45 (38 requested) atoms. Cycle 32: After refmac, R = 0.2120 (Rfree = 0.000) for 2580 atoms. Found 38 (38 requested) and removed 35 (38 requested) atoms. Cycle 33: After refmac, R = 0.2067 (Rfree = 0.000) for 2578 atoms. Found 38 (38 requested) and removed 34 (38 requested) atoms. Cycle 34: After refmac, R = 0.2020 (Rfree = 0.000) for 2580 atoms. Found 38 (38 requested) and removed 31 (38 requested) atoms. Cycle 35: After refmac, R = 0.2001 (Rfree = 0.000) for 2585 atoms. Found 38 (38 requested) and removed 26 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2597 seeds are put forward Round 1: 225 peptides, 2 chains. Longest chain 140 peptides. Score 0.836 Round 2: 226 peptides, 2 chains. Longest chain 122 peptides. Score 0.838 Round 3: 226 peptides, 3 chains. Longest chain 140 peptides. Score 0.830 Round 4: 227 peptides, 2 chains. Longest chain 149 peptides. Score 0.839 Round 5: 220 peptides, 4 chains. Longest chain 101 peptides. Score 0.813 Taking the results from Round 4 Chains 3, Residues 225, Estimated correctness of the model 97.1 % 2 chains (222 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 156 A 2 chains (227 residues) following loop building 1 chains (224 residues) in sequence following loop building ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2453 restraints for refining 2548 atoms. 573 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2262 (Rfree = 0.000) for 2548 atoms. Found 37 (37 requested) and removed 42 (37 requested) atoms. Cycle 37: After refmac, R = 0.2124 (Rfree = 0.000) for 2538 atoms. Found 37 (37 requested) and removed 28 (37 requested) atoms. Cycle 38: After refmac, R = 0.2037 (Rfree = 0.000) for 2546 atoms. Found 37 (37 requested) and removed 24 (37 requested) atoms. Cycle 39: After refmac, R = 0.2013 (Rfree = 0.000) for 2553 atoms. Found 38 (38 requested) and removed 32 (38 requested) atoms. Cycle 40: After refmac, R = 0.1989 (Rfree = 0.000) for 2553 atoms. Found 38 (38 requested) and removed 30 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2561 seeds are put forward Round 1: 226 peptides, 3 chains. Longest chain 105 peptides. Score 0.830 Round 2: 226 peptides, 2 chains. Longest chain 140 peptides. Score 0.838 Round 3: 226 peptides, 2 chains. Longest chain 140 peptides. Score 0.838 Round 4: 227 peptides, 2 chains. Longest chain 181 peptides. Score 0.839 Round 5: 226 peptides, 2 chains. Longest chain 140 peptides. Score 0.838 Taking the results from Round 4 Chains 2, Residues 225, Estimated correctness of the model 97.1 % 2 chains (225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A 1 chains (227 residues) following loop building 1 chains (227 residues) in sequence following loop building ------------------------------------------------------ 28226 reflections ( 99.73 % complete ) and 2456 restraints for refining 2528 atoms. 561 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2309 (Rfree = 0.000) for 2528 atoms. Found 37 (37 requested) and removed 42 (37 requested) atoms. Cycle 42: After refmac, R = 0.2157 (Rfree = 0.000) for 2518 atoms. Found 37 (37 requested) and removed 26 (37 requested) atoms. Cycle 43: After refmac, R = 0.2084 (Rfree = 0.000) for 2521 atoms. Found 37 (37 requested) and removed 28 (37 requested) atoms. Cycle 44: After refmac, R = 0.2072 (Rfree = 0.000) for 2524 atoms. Found 37 (37 requested) and removed 25 (37 requested) atoms. Cycle 45: After refmac, R = 0.2053 (Rfree = 0.000) for 2532 atoms. Found 37 (37 requested) and removed 22 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.29 2.42 NCS extension: 0 residues added, 2547 seeds are put forward Round 1: 225 peptides, 4 chains. Longest chain 86 peptides. Score 0.820 Round 2: 224 peptides, 3 chains. Longest chain 106 peptides. Score 0.827 Round 3: 225 peptides, 4 chains. Longest chain 108 peptides. Score 0.820 Round 4: 224 peptides, 4 chains. Longest chain 109 peptides. Score 0.819 Round 5: 225 peptides, 5 chains. Longest chain 79 peptides. Score 0.811 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 221, Estimated correctness of the model 96.7 % 3 chains (219 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 89 B and 94 B Built loop between residues 123 B and 127 B 1 chains (226 residues) following loop building 1 chains (226 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 28226 reflections ( 99.73 % complete ) and 1886 restraints for refining 1846 atoms. Observations/parameters ratio is 3.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2757 (Rfree = 0.000) for 1846 atoms. Found 27 (27 requested) and removed 0 (27 requested) atoms. Cycle 47: After refmac, R = 0.2570 (Rfree = 0.000) for 1846 atoms. Found 27 (27 requested) and removed 1 (27 requested) atoms. Cycle 48: After refmac, R = 0.2424 (Rfree = 0.000) for 1846 atoms. Found 19 (28 requested) and removed 0 (28 requested) atoms. Cycle 49: After refmac, R = 0.2342 (Rfree = 0.000) for 1846 atoms. Found 12 (28 requested) and removed 5 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:23:12 GMT 2018 Job finished. TimeTaking 60.37 Used memory is bytes: 4484288